I'm not sure apologizing is the right action, if you're not the one who did wrong. I'd much rather hear something like:

This (and here's a list) is why I disagree with these people and these are the steps I'm taking in my own sphere of influence to try to combat this sort of thing (and here's another list). I cannot promise that they'll ever stop and they will probably keep on being the loudest and most politically active Christian voice.

It doesn't serve our purposes to denounce them as non-Christian - we don't define membership this way and nobody would listen to me anyway. I do denounce their actions as inappropriate. At the end of the day, whether or not they're "real Christians," I believe that they have done wrong, and that's what I'd like to focus on.

I am not asking for forgiveness for myself or them - they're not sorry, and I'm feeling sorrow, not guilt. I am trying to express that what's been done makes me sad and I wish it hadn't happened that way. I know this changes nothing practically, and I'm sure you've heard similar things from people using you to make themselves feel better.

I do, though, want you to know that we're not all like that - not because I want to clear the Christian name, but because I don't want you to think you're completely surrounded by people who hate you. Some do - I'm sure you get enough negativity in the average day. I'd like to be just one positive, and I hope I'm one among many. Maybe one day conversations like this won't be necessary, but I feel like they still are.

I do not know how to solve the problem quickly or permanently, but if there are different ways I could help, including shutting up, please let me know.

Something like this. You don't apologize for something you didn't do, and you don't apologize for something done by someone else who isn't seeking forgiveness. You don't promise what you can't deliver, and you don't try to do more than you can as an individual. But you indicate that they can at least temporarily relax. Maybe just for a second, before the hurt comes crashing back in, but you can't force healing.