I don't think malignancies are horrible. Our Psyker got one (just the one, grumble grumble) which gives him a hatred for the dregs of the lower classes.
This is great fun, because whenever they go "slumming" among the downtrodden (which happens a lot when you go inquiring into things related to crime, cultist activity and hidden underground facilities) he cannot keep himself from insulting the locals, sneering at whoever they are talking to, making sarcastic remarks about their usefulness etc etc etc.
Maybe not directly beneficial to their investigations, but it creates all sorts of interesting encounters that we as players around the table find very amusing
As for the Talent, I haven't really thought about it. Depending on your acquisition of CPs this may end up giving you helpful bonuses to many a test, tests which as you say have some permanent negative consequences.
The threat of corruption and damnation is really the only thing that limits and holds back Psykers, and I really do not want to give'em any more chance to avoid the GM royally screwing them over.
Tarald - The Dark Lord of Smeg
You're not drunk if you can lie on the floor without holding on
My House Rules for using Only War (and more) for Dark Heresy games