That's hard to say, there are always going to be people reading more into things then you intended. Look at all the dissections of Shakespeare saying his plays are all about supporting the royal family, or making fun of them. The same thing is true about Moby-Dick, Catcher in the Rye and any other popular book. Even Harry Potter has been subjected to this, both for support witchcraft, and as an attacking on the previous government.
Even worse there is a group of thought that these things are still there even if the writer didn't intend for them, or actively tried not to put them there in the first place. The idea that the intent of the author doesn't matter personally bothers me.
Personally, I would take them aside and tell them that wasn't the case at all, that you didn't base anyone on anybody, and the fact that they acted 'wrong' helps prove this. And that, in the end, it's just a story. If they have a sense of humor about it, tell them it's all wrong and given them the craziest explanation you can think of, but from the sound of it that wouldn't work for these people.
In the end though, all you can do is tell them that they are wrong, and then try to ignore them.