If I did the math right, pitching game 3 would mean he could pitch game 1 NLCS. Pitching game 4, he could not.
Good point. On the other hand, if we're luck enough to be up 2-0, holding off on using him in game 3 (and starting Tanner instead) provides the potential for not needing him at all in the NLDS, so that he could really rest the hammy until the NLCS. If it's 1-1 (or, gasp, 0-2), then you definitely use him in game 3 if he's healthy enough to pitch.