Probably. As has been noted, Clemens is a bit of a *****. I've heard rumors of McNamee having a sick or disabled kid and Clemens refusing to help him with some medical bills. Clemens obviously fired him at some point. McNamee was questioned about 'roids and I have no doubt that he was told he had to give up a big name to escape jail time. At the end of the day, McNamee has a lot of demons and every bit of him screams "weasel". After all, why even mention Clemens? If the feds had something, they don't need McNamee.
If Clemens said "Brian, I need something to get me going" that doesn't mean he knew what it was. He may not have asked because he may not have wanted to know. Therefore, to him, he took B12 shots.