Good question... Yes, my friend has cheerfully referred to herself as a fag hag on a few occasions, and I know that when I use the word I don't mean it in a derogatory way. Having said that, I have sometimes noticed that others seem to have different associations - while I just consider it to mean a straight woman with lots of gay friends (which was the sense in which I used it in this thread), some people interpret/use it as women who hate straight men or are single and bitter, having given up ever finding a relationship and therefore surround themselves with gay guys.
You're right - I'll be a bit more careful about using that term in the future!