First of all, yes, some of the story quests are pretty tough. Part of the problem (challenge?) is that you haven't yet had a chance to familiarize yourself with the mobs you're facing, so you don't know how they telegraph their nasty abilities. In a sense, dying in such a situation is not very different from dying on a new boss in WoW: you're climbing a learning curve. The important part is that you learn from your deaths and apply the experience to the next attempt.
That said, there are a few things that you can do regardless to even your odds.
Especially when facing a bunch of melee mobs, you should not just be dodging when you see a nasty attack, but you should be moving constantly. A lot of attacks will just miss if you're not standing in one spot all the time (though that is less true for ranged mobs). Many mob attacks have a wind-up time that is longer than it takes to strafe out of the area. Even if you're running with melee weapons, you want to strafe/circle-strafe a lot.
Don't just rely on dodge to not being hit. Use abilities that block, blind, stun, weaken (with the latter two, especially the ones that can do it to multiple targets). Thieves also have a number of attacks that provide dodge-like evasion to preserve endurance.
Watch your health. Use your self-heal as soon as it's not wasted, don't wait until you're actually close to death. The sooner you use it, the sooner it comes off cooldown again.
Finally, level matters on some of these personal story missions. There can be a big difference just from being one level below the recommended one instead of one level above.
just a thought: do you wear level appropriate gear? I really (most of the time) forgot to check my gear before visiting a story-instance. Those instances seem to be balanced around a specific level (the number in brackets on the top right of your screen) and you will be scaled back, but not scaled up to that level. Maybe your gear is simply too bad?!?