hmmm. That's a good question. I did some research last year when the drs were telling me that I might have a fistula on top of the absccess. It really depends on the type of fistula. If it is not too deep the dr usually lays open the channel so that there is no place for the bacteria to get caught. If it tracks between your internal and external sphincter, the drs. usually insert a seton which slowly cuts through the sphincter and lays open the infected channel.
There are other options though. One as I mentioned is the fistula plug, though this might be difficult to set in place if there is only one opening. Another, which sounds more appropriate for you, is fibrin glue. this is basically a bio-glue made from your won blood plasma. It's success rate is lower than traditional fisulotomy (laying open the track), but it seems like a far less painful option. basically, the dr cleans out the track with a bit of scraping and then squeezes in the glue and sews the opening shut. Take a look at this article
http://archsurg.ama-assn.org/cgi/reprint/135/2/166.pdf. There are some video sites on the web, but you can google those if you're interested.
This is really the extent of my knowledge. The most important thing for the dr to do is make sure he finds all of the tracks and treats all of them. There may only be one opening, but the opening can have moer than one path. Most of the reoccurrencce of fistula is due to the dr not finding a track.