I might not have thought this through entirely, but with many vets entering the PVP’s just for alliance points and selling the 3* covers as they have fully maxed them (often), why not split the events and have one event for 3* covers and another just for ISO (e.g. 600 ISO per cover that would have been earned) - then at least transitioning players have a chance to get something that is needed and alliance points are still kept.
I would tweak this idea a little bit and say that the alternate PvP would offer double iso for each battle. I would definitely do that one when I don’t need the covers. Just replacing the covers with 600 ISO isn’t enough of an incentive to do something different.