Yup, it's a two-step change:
A. auto-explore never chooses a revealed pirate base as its target
B. units always avoid a pirate base when pathing unless they literally cannot get to their destinations without passing through it.
Would be very nice; I often have to queue up orders to ensure my units go around pirate bases. Sometimes the "predicted" path shown is not the one they will actually take, which gets really annoying since post-Diplomacy pirate bases are significantly more dangerous to units that are just passing through.