Norton to Ruffalo is exactly the way to do this.
Whedon wasn't tied down by what Letterier had done, he mixed up the design and the Bruce characterization and general tone, but it was done in a way that if, hey, you liked The Incredible Hulk it's not totally stricken from the record either.
They just sort of move forward without canning what came before, and if some director down the line wants to reference The Incredible Hulk they can, if not they're hardly bound to do so.
Exactly how you go about the Batman thing. Give Reeves all the freedom in the world to do as he wants, change things up, have a different take on Bruce & Bats and the world, but just don't even acknowledge it on screen at all - don't do the Flashpoint change-up thing, it's not necessary. Just a change-up, maybe a smartass line of dialogue acknowledging it like they did with Rhodey in Iron Man 2, and be done with it. It's the Reeves & Gyllenhaal show now, we don't even bother explaining the change-up, but also not go out of our way to ****-can what came before.
Best of both worlds. Us who don't like the Snyder/Affleck take can pretend it never happened, those who do like it can just Keaton-to-Kilmer/Norton-to-Ruffalo the damn thing.