So since I never unlocked Heavenswards Alliance, and have only unlocked the first step of Stormbloods what im hearing is...just leave them locked. Then even if SE ever implements some kind of anticheese it has basically no effect on me anyway lol.
They're totally worth doing once. Weeping City and all of the SB raids have neat aesthetics.

But if you want to avoid doing them again in the future, there's always the item level cheese... unless SE eventually does decide to do something about it, anyway. However, I imagine that whatever they end up doing will involve requiring you to have all the dungeons for your particular level unlocked (as well as sufficient gear to actually enter all of them), meaning that simply avoiding unlocking the dungeons may not help you get around whatever measures they implement.