Arcian wrote...
^Guess that answers it.
By all means, correct me if I'm wrong or you saw something different in the script!

I specifically remember (major spoilers for Prothy, as always may not be accurate now):
Shepard asks Prothy about the crucible plans, and if he has any idea what the weapon does or how to make it. He only heard of it, but never saw anything about how to make it (he's a warrior, not a tech or scientist), his mission was to rebuild the Prothean Empire after the Reapers were done sacking it. He would then prepare the next cycle to fight the Reapers, however he was betrayed by indoctrinated Protheans. He is similarly clueless about Ilos, though he knows that it was doing something important.Over all, I think killing him would be a shame and a waste, as he's got a whole bunch of cool dialogue from a very nasty perspective on your squad mates, and calls many of the Gary Stu/Mary Sue characters out on the carpet.