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I know what you mean Foot56 and I wouldn't recommend Crossfire with a non-reference-cooler card for the reasons you mentioned - the cooler will exhaust the air onto the second card / into the case and the second card will feed hot air to the first one. The reference AMD coolers try to push air out of the case rather than into it, which simply works better for Crossfire.
That's not to say your cards won't manage. I'd just prefer the reference option because it may also mean less overall heat in the case.
as long as you have adequate cooling it shouldn't matter if they exhaust in the case or out of it. a single side fan on a case will take care of the issue of the top card drawing in hot air.
Would it be a bad idea to run ASUS 7970 DirectCU II in crossfire? Im just thinking about the temps of the first card not being able to suck up air? Has anyone does this yet?