And snuffing Doom was utterly the right thing to do. Fuck all that psycho history stuff, Ultimatum was something he could never ever be allowed to walk away from.
I don't have any issue with killing Doom, although I think it was done a bit too easily. (And I'm sure it'll be revealed to be a rogue Doombot sooner or later.)
That said, I can't really see Ben killing Doom. If anyone in the FF was going to do it, the only person I could see stepping up would be Sue. I think it's a lost opportunity turning Ben into this dark killer, and then further contorting Reed's character to justify it, when you already have someone who's smart, capable, and has a personal motive for offing Doom in the death of her father.