As far as I know, there are ten (10) factions in this game, some not specifically called out, like the "Bank Faction" in Arnika (Llorac and the Bank Guard, while Llorac can call help if threatened). Also, the Rapax seem to have a separate faction, the "Assassins" or whatever, that wasn't fully implemented.
What is on display, is the ten (10) factions:
Brotherhood of the Ascension
Higardi
Trynnie
Mook
Umpani
T'Rang
Rattkin Common
Rattkin Razuka
Rapax Common
Rapax Templar
The first six (6) factions seem to be peaceful, and a party that wants to be Cosmic Lords would treat them respectfully (even though the Umpani and T'Rang are at war, they hint that they may not hate each other that much, and would rather focus on their common enemy, the Dark Savant).
The last four (4) factions, not so peaceful. The Rattkin came to the planet Dominus for money (to get $ from the Dark Savant, and also stole the 6th Bough from the Trynnie), and the Rapax are a warlike race, focused on planetwide domination, led by their cruel mistress, Al-Sedexus.
So, since the Rattkin Common start out as neutral towards the party (nothing can be done about that, to make them more friendly), whacking the Breeders stands as fair game (the Trynnie hired me to take them out, so they can regain the Sixth Bough).
Whacking Rattus Rattus removes the question of what happened to him (he died by my hand). However, this makes the remaining two (Milano Calzone and Don Barlone) hostile. Oh well, I guess I will have to clear out the Sixth Bough for the Trynnie (while gaining the Astral Dominae for free).
The Rapax Common attack you on sight (both outside of Trynton, and in a set battle in the Upper Branches), so there is no way of making friends with them until way later (until you do the deed with Al-Sedexus). So no guilt there.
The Rapax Templar are a special faction (they will even tell you to stay away from their Rapax Away Camp), without attacking you. I guess that you can make them hostile by approaching them, but I believe that all Rapax will attack you if you kill Al-Sedexus and her support (though you can bypass this by killing her directly, before she casts reinforcements). However, there is a point in the game, on Ascension Peak, where you have to kill Al-Sedexus's daughter, and the Rapax Prince, so there is no permanent peace with the Rapax.
Also, Crock the kidnapper. Killing him is fine. Nobody cares.
Finally, the drunk Rapax Constable. He's drunk, he's not doing his job, and he holds a key that I want. He probably won't even feel the killing blows.

Add:
Unaligned
Party
Dark Savant
Cozmik Lords
Higardi Bank
Higardi HLL
Mad Marten
Rapax Army and Rapax Asssasins
for the complete list.
(note killing member of "unaligned" faction does not appear to drop ratings for other unaligned entities)

Besides, you can completely avoid the spawn of the Rapax Army at AP, incl the Prince,
and in case you did not avoid having sex with Al Sedex, also your child,
set a portal at AP, e.g. behind the big Rock where you find the mana stone,
before you enter with 2 of the 3 artifacts in inventory AND before Braffit tells you about the landslide.

There is no clear evidence for Crock kidnapping a character, not even in any of the game files,
so if you use the suspect to justify that for lkilling him, you cant be playing the good guys.
Fortified by the highly questionable justifcation for killing the Constable,
that means, drastically exaggerated, whenever anybody, incl you, is in a state of not feeling it,
it would be ok to kill the person for unethical reasons.

Perhaps i should script a penalty for killing Crock and the Constable,
like drop of rating for multiple factions that could potentially like one of them,
or bad luck on next 1D100 rolls etc pp :p

Ok. I get it. You're German, or European, or whatever floats kids these days. English isn't your primary language. I respect that you are trying to learn English as a secondary language.
Killing Crock and the Rapax Constable are questionable. How about, I kill them quickly, painlessly, with instant death attacks? The Mage has Asphyxiation, the Alchemist has Death Cloud, the Priest has Death Wish, and both the Priest and Psionic have Instant Death (the Gadgeteer has a gadget that does the same thing, the Vaporizer).
In this way, they would feel no pain, and I would lose no faction rating (who keeps track of these things anyways, the Cosmic Lords)?
I don't understand those who love Rattus Rattus. He is part of the Rattkin mafia, and literally could have sentenced me to death if I had been a lower level party, about to rob the bank with his letter. He also disappears, probably part of an unfinished quest, so I might as well know where he went by whacking him (he IS part of the Rattkin Mafia, not a good guy by any means).

I have a psychic party, that can read minds. I can see that Rattus Rattus gives the party a stick-up note, because he's lazy and doesn't want to do it himself.
I can see that Crock is old, too old for combat, and he wants to kidnap a character to kill Brekek, a frog that he wants to kill for whatever reason.
I can see that the Constable is too drunk, and unfit for duty, so he shouldn't be holding the key to something so important.

Have you tried the Mindread spell?

One use of that spell that I found was to use it on Sargent Kunar. Cast it at Power Level 7, and if you get it to work, try telling him what his thoughts were.

(Might want to save first, as this may result in losing access to a merchant. Also, you may need to guess the answer to a question, but it's reasonable for a first time player who's explored other parts of the game to guess it correctly.)

Usually, when I talk to a NPC, it's all business. I ask the standard questions, not wanting to waste the spell points with the Mindread spell. Once you get to a certain point, Communication skill requires you to talk to 3 new NPCs for a skill up.

Except that, when you're interacting with an NPC, you're generally in a safe place where you can rest.

In fact, the only real danger that could come up is if your Mindread spell backfires and makes the NPC hostile. (Note that a backfired Charm or Mindread may, depending on the NPC, make it neutral instead; I've had that happen with Lord Braffit, for example.)

Someone playing the game for the first time might be curious about Mindread, and discover that thought of Kunar's.

Here's the *spoiler* description of what happens:

* You successfully cast Mindread PL7. The thought is "Destiny Arrives Tonight".
* You say "Destiny Arrives tonight".
* He asks, "who sent you"?
* At this point, you have to guess, and if you guess wrong, I believe Kunar becomes neutral.
* A perceptive player might get the idea, given the reaction, that Kunar might be a T'Rang spy, and might know that the T'Rang quest giver is Z'Ant (particularly if they've also started the T'Rang quest line).
* With that answer, you've done the first part of the final T'Rang quest. You have the fake keycard (which can open all the high security doors), and your characters now know Z'Ant is a spy.
* What you do next might depend. Not sure if you can destroy the Umpani ship without getting the quest from Z'Ant, but I do know that one possibility is to turn in Kunar for a huge XP award. (Just be careful, as you may gain multiple levels if you do this at a low level, but your skills won't have improved.)

By the way, does Mindread reveal anything interesting when used on Rattus? Or Crock, for that matter?

Nobody knows. I don't think that anybody wants to mess up their game that way, but you feel free to experiment. I am trying to build up a MDP that is so powerful that nothing can stop it.