Why does she get "bummed out" by your husband? She won't be bummed if she doesn't see him. If the being bummed is because you can no longer spend time with her like you once did before marriage, she will have to learn to work through that as a fact of life.
Keep the two of them separate. It sounds from the post like you are spending time with both of them together, which is asking for trouble. Going out with her doesn't have to involve him (I'm assuming here he is willing to watch the kids while you have the occasional afternoon or dinner out with her...?). Going out or staying home with him doesn't have to involve her (you know they don't get along, so don't invite her to the house when he's there). And going on vacations with both of them? That must be so tense for you and for them too.
If she's asking to go on vacations with your family, that sounds like she may be a bit needy -- craving your company so much that she will, as you put it, tolerate him. Ask yourself -- Does she cling to you in other ways? If you looked at the relationship from outside, objectively, would you say maybe she is at your house more than most adult friends, even best friends, really should be? Does she have other things and other people and other support systems in her life, or does she depend on you? I am not saying that's the case because it's hard to tell from a post, but it's worth thinking over.
It's great to have friends who are different from each other (and I'm listing your husband as a friend here!). It adds interest and different opinions to your life. But it sounds like she is getting in the way of your marriage, and/or your husband is getting in the way of your friendship. Trying to "make them see better eye to eye" will cause you a lot of stress and grief and isn't your job as a wife or a friend. Think about how you can see her a reasonable amount of time, without him, and definitely I would reassess the idea of vacations with both of them.
