I don't know what his full position on abortion laws is, but here he is only arguing that government should not be able to force doctors to perform abortions. You can't argue with that.
He also is fine with gays having the right to marry, so I think you misread him. But if you think that you should have the right to dictate to the Boy Scouts who they take for members, you are clearly in the wrong. The Boy Scouts cannot violate anyone's rights. You don't have a right to membership. "Civil rights" is an anti-concept. There are only individual inalienable rights, and that includes the right to associate with whom you wish in your personal or professional life without the government overriding your judgment and forcing you to associate.