Its all hierarchy-based, so if its applied to the group at the root itself, the children will inherit it and I don't believe there's anything you can do. If you're applying the gradient via code, you just have to make sure it gets applied to the art you want it applied to.
If its being applied by a user outside of your plugin group, and its being inherited into your plugin group, I'm not sure there's anything you can do about it. I'll take a look though, maybe a group can opt out? I'm not sure. Plugin groups do have their own set of rules, but I think that mostly applies to geometry, not appearance. I could be wrong though.