Yea, OmniFocus doesn't do any kind of clean up on the backed-up files. A few people have already asked for a new feature to do this.
Until such a feature becomes available, I've been using the
Hazel preference pane to automatically remove any backup file older than one week. This isn't perfect, but it's a pretty good/easy way to get 95% of the desired functionality. Note, however, that Hazel is not free ($22 USD), but it's also useful for a variety of other tasks and has a very nice GUI.