I wouldn't necessarily want to mill the heads to compensate for the block being decked. Then you've got an even more expensive set of parts married to one block. I'd rather cut the intake in that case.

Let me clarify...If all you do is deck the heads and then cut the intake face...they're good to go on anything.
But w/ the combination of heavily decked heads AND the block too...even if the top of the block has been cut to compensate, it will need to be mocked up to see.
If there is still a mismatch, I would not cut the heads more to make it up...rather cut the intake.