Unfortunately, there is precedent for tweaking the WW mythos and Donna's origins without a wider DCU reboot. Which can be a positive, because DC needs to learn to not reboot all the time or draw so much attention to fixing crappy elements of their lore. Pretending all the crap Abnett has been writing didn't happen doesn't need a lot of fanfare. Just establish in a page through exposition that Donna is Diana's adopted younger sister and call it a day. That doesn't solve what to do with Donna and her whole generation NOW when they are the redundant generation between the JL and the younger kids, but it would make her relationship with Diana less of a headache.
I don't think Doomsday Clock is going to impact too much on the WW side. I don't see any practical reason they should change anything in Rucka's run. Nothing's broken, and getting Wilson on WW was a big get for them, and she's already building off of Rebirth arcs. Stuff like Jason just needs to be ignored, they need to stop using a sledgehammer to kill flies.