Recasting isn't a bad idea in the least. It's actually quite a fantastic idea.
Firstly, it separates the JLA movie from the Superman and Batman movies. If it does end up being bad or too fantasy based or whatever, it won't be tied to any of the other films. It won't lessen them or ruin what they've set down like, say, B&R did to Burton's Batman movies. Instead, JLA can exist in it's own little bubble.
Also - while I'm really digging - is it gives someone else a chance to really excel with the characters. Sure, Bale and Routh were great, but I'm honestly really excited just to see what two other actors will be able to do with the roles. Who'll be Batman? Who'll be Superman? Will they be more Keaton than Bale? Or Kilmer than Clooney? That unknown and that chance at having something really great and different happen is a great thing.
I would agree with everything you said if the current Superman and Batman series were over but doing this right in the middle?
Makes me wonder if WB is trying to sabotage Nolan's and Singer's series and if not then thats what they are inadvertly doing.