A number of times I've been offered quests which involves destroying a certain ship (because it spoils the Gaalians' psi-flow, because it carries an animal poacher, etc). In my experience, they all too often turn out to be a liner/transport/diplmatic ship, and only rarely some pirate.
My problem is that, being an all-around good guy, I'm not really keen on hunting down civilian ships. Is there really no way to fulfill such quests without eliminating the ship in question?

I understand they do, but it's still annoying that they dress up killing civilians as something exalted and noble - or rather, that the game puts indeed-malicious elements on otherwise innocent ships.
Thanks, that answered my question.

For a while I was convinced one of the races was out to destroy my already soiled reputation with the Maloqs because they kept sending me after their ships. They would say oh he is such a bad guy you need to get him, but when I blow the guy up its oops. Turns out he wasn't such a bad fellow but here is the money. There were places I couldn't go without having an army chasing me down. That part didn't last too long though because once you start saving star systems everyone's opinion of you starts to improve.

In the end I was just glad for missions I could do. I found doing most missions frustrating especially the text based ones.

Ah, yes, poorly-translated texts which can even confuse you regarding what to do ("DND player", I'm looking at you).
Nowadays (the in-game year being 3326), I mostly get "shoot this civilian ship"-quests (which I decide to not take), some text adventures and protection missions. The last are especially good when you're tasked with protecting a liner which just goes on its way and is left alone by pirates; in that case, you can mostly go about your business and get your reward when your contract expires.

SR2 is much deeper than gamers understand, I believe. I think this is because the game is 2D and has a humour about it.

Quite simply if you think various races won't try to manipulate you and use you to their own ends, you will be taken for a ride many times - and pay the price for it. Races have changing reputations with each other and as your reputation changes as you help/hurt various races, so the variables become quite deep and you have to keep your ears to the ground! :)

To this day, 15 years on, many people think the blackmailing that goes on in Daggerfall is a bug, not code written.But blackmailing CAN happen because of the procedural way the game was written allowing for emmersive moments.

The same goes for the procedurally written SR2! :)