Hmm...I find it really strange that you feel you have to make up a story rather than be honest! I don't see the problem in saying how you met online. Who cares if people make a big deal out of it or find it odd...in this day and age, it's really not unusual at all.
We did the same thing for years. We met years ago, so the fact that it was slightly less accepted than it is now might have been a factor. I am generally a pretty honest person, but I don't feel I have to explain myself to people who I barely know. Our family and friends knew how we met. Acquaintances and curious shopkeepers, distant relatives who barely know us, fellow bus passengers, receptionists, etc., etc. (we're talking the States, so people are much more likely to ask probing, personal questions) got the story about meeting when my husband was doing his internship in the States.
It's not that I minded people knowing. I didn't like the follow up "advice", comments, predictions, and so on. I don't feel guilty. It's more polite than saying "none of your business" and "it's a long story" only goes so far sometimes.
We now say where we met, but I don't blame people for being reluctant on being totally honest, really.
I think that you can't know someone if you've just met them online. I totally agree with the common wisdom on that. You do have to spend time in person because you can easily fill in the gaps to create a person in your mind nothing like the actual person. Or he or she can do it for you, either consciously being deceptive, or trying to emphasising their best bits without being obvious about their worst. You need to spend a bit of time in the flesh, knowing how they react to things, what they are like, and if you are compatible. It doesn't happen all the time. My husband and I are good examples of that. Both of us were exactly as we figured, which surprised me a bit. However, after meeting, there's nothing "unreal" about time spent online.
In a few weeks we will be celebrating our 10th anniversary. My father-in-law made a comment the last time he was here about how that was different than being married for 10 years and living together that long. You know what? He's right. It is different, but that doesn't mean it was easier. My sister told me constantly while my husband and I were in an LDR that it wasn't the same as sharing a life and the stresses and arguing over which orange juice to buy. She was right. It's not exactly the same, but there are a lot of very hard obstacles people in LDRs have to overcome that people in close proximity relationships never do. And just like in close proximity relationships, if you can overcome them or at least deal with the problems, it tends to make the relationship stronger in the long run.
We've spent just under half our marriage in an LDR (if you count all the trips to the States and my time here so far). I've gotten to the point where I don't care what people think or say about it, but when I was having to deal day to day with being apart, I didn't need the added stress of constantly explaining myself or being told "Oh, long distance things never work out." Or any implications about what my marriage is about because of how we met or spent the first part of our live together.