Arkose: A crucial reason for such an option going away is that they have moved away from morally flexible protagonists with uncertain futures to protagonists that are fated to be the good guy in the long run and can only do slightly questionable actions along the way for the greater good, sort of like a pussified Jack Bauer. Killing a companion falls a bit too far off the side of evil for Pussy Bauer, especially since the companion's questionable morals were typically known when they joined but brushed over with a "use the tools of evil to fight evil" speech.
You can kill Zevran at his ambush. Tease Leliana mercilessly about her beliefs then take her to the Gauntlet so she can watch you piss in Andraste's ashes and then you can kill her (and possibly Wynne too).
Speaking of Wynne, I've decapitated her a few times at the Circle Tower.
Arkose: Unfortunately, BioWare's "ends justify the means" options generally backfire because very few allow you to make significantly debatable decisions (like letting some innocent people die in order to potentially save more lives in the long term); most of them involve small-scale acts like fleecing a widow out of her dead husband's possessions or demanding more money for a job, things which simply aren't going to help the war on terror (replace with Darkspawn or Reapers as appropriate) in any tangible way and just make Pussy Bauer look like a total jerk.
You can burn Amaranthine to the ground with all survivors still in it, to retreat to the more defensible Vigil's Keep in Awakening.
Arkose: Having companions able to be killed off also complicates matters when it comes to DLC and series continuity. Mass Effect 2 allowed saves to be imported, which was a nice touch, but if a person had been killed on your save they are replaced by a conveniently equivalent character, minimising the long-term significance of that character's death (in terms of both plot development and gameplay functionality).
Ordering your lover to die on Virmire isn't negated of all impact just because someone with an assault rifle joins your team in the sequel.
Letting Wrex live significantly changes the story/future of Tuchanka, if not the gameplay there. Plot & story changes at the fringe, over wild experience changes will always be the norm due to the costs of development.
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To the person who disliked Morrigan because they left and Alistair insisted on landing the killing blow... I think this was addressed in a patch? It started as a fan mod but (I could be wrong here) I think it was added in either 103 or 104, you can insist on making the sacrifice as a female warden now.
My biggest gripe as a noble born female who suffered (tremendously) through the terrible Alistair romance was that he refused to marry prior to the final battle. I so wanted to metagame him dead at the final battle and rule as queen alone. If he'd had the fucking stones to kill Anora (whom I actually love as a character) then I could have made a play for the throne afterwards, marriage or no... I HATE Alistair... and I'm getting side tracked.
