On the contrary, I think one absolutely has grounds on which to agree with one while disagreeing with the other. Having moral discernment isn't hypocrisy, and if one genuinely believes that one is a good policy while the other isn't, then there's nothing massively, or even slightly, hypocritical about taking such a stance.
What would be hypocritical would be to say that only one set of people should ever be allowed to engage in civil disobedience while others should not.
If you truly believe in your heart that a particular set of laws is unjust, I don't think you'll find very many on the left who will chide you for civil disobedience in and of itself. They may not like the cause
it is being employed for, but it is not the disobedience as such that is the issue. It is the American right that, in my experience, fetishizes following the law solely "because it is the law."
In other words, one can disagree entirely with the aims of these localities while at the some time recognizing that such disobedience is something sacrosanct that should be an option open to any people who wish to take a stand in accordance with their morals and their principles.