First of all I'm incredibly happy that you and your friend both have feelings for each other. I know what it's like to have desires like that and being unable to express them for a long time, so it's awesome that the both of you get to explore that part of your relationship.
My advice? Talk with your friend. I know you don't want to hurt her boyfriend - but in my mind you need to really see where she stands on this development. The both of you have cared for each other for a long time and you both finally came out to each other. In my eyes that's a HUGE thing. Feelings and emotions aren't like actions and sex - Her boyfriend can't request that you two stop loving each other... and to say that you two can be sexual active together, but to refrain from being emotionally involved is a bit naive I think.
So talk to her, determine how she feels. If she wants to support her boyfriend's desires then you need to cope with that and the two of you can come up with ways for you to do that best - maybe that means the two of you stop having sex? I don't know but you should both figure it out.
However, maybe her feelings for you are more important than the desires of the boyfriend. I don't mean to make it sound like a competition or anything - but when two people have conflicting desires, especially extreme ones - someone has to "win". So currently, The boyfriend doesn't want the two of you to date seriously, however... you DO want to date her seriously...
Logically, the only step is to see where she stands. If she wants to date you seriously, the the two of you need to figure out how to approach that with the boyfriend. He'll either be compromising or he won't be. In this situation, at least one of you is going to have to deal with loss of some sort. So communicate and figure out who wants what, versus who can HANDLE what.
If there was a deeper level of honesty between your friend and her boyfriend, then he might have been aware of this possibility when he ok'd a sexual relationship between the two of you. If he knew the history between the two of you to the point of the emotional level - he should have known to deal with the fact that you two might be serious.
Hope it works out.