Not exclusively. The current debate is about whether to focus on Islamists in general in Afghanistan or just Al-Qaeda. The question is how much of a threat is the Taliban? Would it allow Al-Qaeda safe havens like it did in the past? As you surely know, the Taliban and Al-Qaeda are cut from the same ideological cloth and share the same goals so I believe it would be a mistake to allow free rein to the Taliban.
Yes, it was profoundly stupid for Bush to divert resources from Afghanistan for an unnecessary war in Iraq, though.