I think its a preference deal.
I would say this, if its a keeper or dynasty situation, it would probably unfair to change it unless every single manager agreed. Using OBP instead of AVG will throw off the value and rankings of players.
Off the top of my head, Ichiro has a .320 career AVG but only a .365 career OBP. So in an OBP league Ichiro's value was far far less, since you have guys like Nick Swisher with career .360 OBP.
On the other hand as a Carlos Santana owner last year, (a guy who's avg was .247 but OBP was .363) There would be plenty of times when he would be drawing those walks and I would just be frustrated because I knew it did nothing for me and his .247 wasn't really an accurate measure of his worth on that team.