Yeah, that was the vibe I was getting from that too -- Reed, realizing his limitations, effectively killed Doom by proxy.
However, I think both Ben and Reed knew that even knowing it had to be done Reed would never be able to outright ask Ben to do it. And think it speaks volumes that (a)he doesn't have to, and (b)Ben's willing to do the deed himself. Though in all honesty I don't think any of the 4 would be able to bring themselves to bring the problem to an arse-hat like Fury or anyone associated with him given what happened when he and Doom teamed up to fuck with Reed's dimensional probes. Ultimately it was a Fantastic 4 problem and Ben was the only one at the end in a position to do anything about it.
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.