I think both these instincts are right. We should feel a little bit weird when we laugh at jokes about a minority group that we aren't part of. It's important to examine our stereotypes and prejudices. Sometimes humor is a good way to open our eyes to differences and make us think about things that we haven't thought about. Good art helps us do that and I consider comedy an art form.
I really love the thoughtfulness you bring to this topic. It isn't a simple one.