Once AFMU finishes repairing a module that's been switched offline specifically by the repair function, it should automatically switch online once the repair is done, especially if there's no collision with power budget which would mean reverting to higher priority power state.
I'd argue that the current behavior that leaves modules disabled until explicitly re-enabled is borderline a bug. If you explicitly wanted module to stay disabled after repair, you could get that behavior by toggling the module offline manually and then starting a repair, which presumably shouldn't re-enable it automatically.
Having to re-enable the module is tedious at least, counter intuitive and borderline confusing at worst. It makes me not want to bother with bringing an AFMU because I know that I'll have to menu-dance and it might be simply less pain to just fly to a station and repair everything; you're already eating into your ships precious internal space to improve your practical endurance with little real help in-combat, it might as well maximize convenience.
I'd argue that the current behavior that leaves modules disabled until explicitly re-enabled is borderline a bug. If you explicitly wanted module to stay disabled after repair, you could get that behavior by toggling the module offline manually and then starting a repair, which presumably shouldn't re-enable it automatically.
Having to re-enable the module is tedious at least, counter intuitive and borderline confusing at worst. It makes me not want to bother with bringing an AFMU because I know that I'll have to menu-dance and it might be simply less pain to just fly to a station and repair everything; you're already eating into your ships precious internal space to improve your practical endurance with little real help in-combat, it might as well maximize convenience.