If you turned the CPU cooler so it was blowing hot air toward the top of the case, there'd no problem. That's how I run mine. Most cases have fans on the top now-a-days, so it makes more sense to do it that way anyways.
There are a few situations that you can't turn the heatsink around. Some motherboard/heatink combos will not work together when positioned that way. Also some heatsinks with heatpipes suggest the sideways orientation for the best performance of the heatpipes. Also every case we have had come in have the 120mm fan positioned to pull the hot air right from the CPU heatsink right out the back.
But if someone did have an issue with the clearance you could move your cpu heatsink around. Honestly with this being focused more on the HTPC crowd, I doubt that the clearance will be a big issue for most. Even with my setup it still performed well.