Perhaps...I haven't run the numbers much to see exactly how it would play out. It would probably depend on when Alabama lost and how they recouped. For example, if Alabama lost against LSU next weekend (especially if it were a very close game), I don't see them dropping much further than maybe 4th in the polls. Considering that a 1-loss Auburn, Missouri, and Oklahoma are all ahead of Baylor in the computers at this point, my guess would be that Alabama would probably edge Baylor out there as well. Then assume that Alabama wins out, including victories over Auburn and Missouri (or USC), I just don't see Baylor jumping Alabama in that scenario.
Now, of course, if say, Alabama, Oregon, and Baylor were all undefeated heading into the Championship Week and Alabama lost, then Baylor would almost assuredly get in. I guess my point is that I think it depends on when Alabama loses as to whether an undefeated Baylor would get a shot.
That being said, I don't see Alabama losing.