Close micing 'is' the way to do it, hence my original post, I'm offering you my 'professional' opinion on the matter.

The length of the clips is inconsequential, in fact, short clips full of background noise are probably going to be more apparent. The only other option I could give you that might prove satisfactory is to take a feed from the PA, which can actually be quite simple and cheap to accomplish.

I would also say that recording the audio separate to the video is not normally recommended these days. It can be a time-consuming process to make sure that everything starts off in sync and, just as importantly, stays in sync during the whole recording. Unless you're going to clapper board at the beginning and end of scenes.