Oh, I agree there's definitely a degree of petulance, if you will, to Mace's comment about the weapons, and I don't think it was indended for the character to necessarily be calling the Doctor hypocritical. It's only after I rewatched the episode, and possibly because I've been rewatching them almost daily rather than weekly, that I think I heard it like that - if that makes any sense whatsoever! Also, knowing what's coming in The Doctor's Daughter, when Jenny challenges him about weapons may have also had something to do with the way I heard that line.

Also, it's pretty clear that Mace is a bit of a Doctor fanboy so I can see he'd be a bit put out by the Doctor's dislike of gune and his disregard for military authority :-)