Reed is super smart, and he knows Ben has always been there to haul his ass out of problems. And since they became metahumans, Ben has shown that he trusts Reed's judgement to the point where he won't question his directions.
So given the dialogue, there's no way that Reed isn't giving Ben a covert order to assassinate Doom. He's laying out the whole situation, making it extremely clear that Doom needs to die, that this would be a good thing, but that he's too weak to do so. If only someone could come and haul his butt out of the swirly/kill Doom!
At best he's manipulating his life-long friend into doing his dirty work for him, at worst the Reed/Ben relationship just went from strong friend/smart friend to master/minion.
Ben killing Doom never sat that well with me in the first place, but this doesn't do anything to make me feel better about it.