Prohibition has caused more harm than good, lack of gun control has caused more harm than good, outlawing encryption would cause more harm than good. There is nothing logically inconsistent about holding these views.
I think the claim is that these views aren't held for utilitarian reasons, rather they are held for ideological reasons (ie freedom). In fact, if we want a pure utilitarian viewpoint we ma find the East Asian model where you get shot for selling drugs to yield the most quantifiable value.
... for narrow definitions of 'quantifiable value'.