My hubs and I met online, but we lived in the same city at the time.
More relavent to your question, though: I met a boy long ago online [way before facebook or dating sites] who eventually came to see me in person. We had chatted an entire summer, and then I agreed to get him from the airport and take him down to the college we were both attending for the fall term. We stopped on the way at my Grandmother's to spend the night [the airport was a good 3-4 hours from our University], and not only did we share a room, but a bed [although a HUGE king sized bed]. We went on to date seriously, move in together, and eventually start to plan on getting married before he revealed to me, quite accidentally, that he was completely homophobic. As a girl with many close friends, cousins, a BROTHER, and a SISTER who are all Gay, that was a deal breaker, obviously.
So the moral of this story is, Yes: I think it will be fine and you can stay together PROVIDED you feel you know them really well and you trust them. It worked out fine in my situation and if I was also a bigot, I'd probably be happily married to that guy! It does take a bit of a leap of faith, but I say stay together. Just be prepared for it to be awkward, maybe. When I met my hubs [after only knowing him online for a week or two], it was very awkward, but after our second date we were thick as thieves and we still don't like to be apart for more than a day--even after 7 years!
Good Luck!