Well, I've rewatched it and there is still no explanation given for Van Gogh being pant-less outside the church. Nothing like 'I prefer to paint with my pants off' or anything.
Given this, one must assume that it is either sloppy editing of some longer scene since annexed, or that it is one of the oddest timed bit of hanky panky ever seen in Doctor Who. I mean, in the middle of stalking a huge, dangerous, alien creature, it's like the moment the Doctor leaves them on their own (to confront the monster in the church) Amy must have said to Vincent, 'Quick! He's gone. Get your pants off!'
It's just odd and incongruous in an otherwise sensical story..