I wouldn't count Lincecum out either, but the fact is that neither one of these guys is likely to continue this pace. They could potentially end up with an ERA under 2.00 at the end of the season, heck, Greinke ended up with a 2.16 ERA last season pitching in the AL.
However, assuming Halladay is relatively close to Lincecum in ERA, he'll probably have a bunch more wins as well as the benefit of playing on a big market team. I really doubt Lincecum would be picked over Halladay for CY it their stats are close.