From what I gathered, he was trying to save his bench. Diaz already came in to relieve Molina, and the game was tied 1-1. He didn't want to use up his 2nd to last bench player in a game that might go extra innings, so he stayed with Marquis who is at least competent with the bat. That being said, I'm not sure I agree with the move, but eh, whaddyado.
...Boston papers now and then suffer a sharp flurry of arithmetic on this score; indeed, for Williams to have distributed all his hits so they did nobody else any good would constitute a feat of placement unparalleled in the annals of selfishness. -Updike