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I haven't tested intercontroller peer to peer blocking, but as said I can imagine this is a controller setting iso a mobility domain setting. That indeed makes it difficult to block if the controller interfaces are in the same VLAN. In my believe this is a theorethical discussion since you can block all peer to peer on neighbour APs on a WiSM, so you should be able to separate between buildings/floors.
I would not want 1.000 APs on a single controller for a number of reasons.
Be carefull with upgrading if the number APs exceed 100 APs on a controller on a WiSM. I have tested a threshold of 117 where APs get queued and you will run out of the service window.