I did some back of the envelope math...and I'm not buying the cost of sensor reasoning.
If Canon is using a 300mm wafer, they will get roughly 80 sensor dies at full frame and 215 sensors at APC-C. (Don't shoot me here, I didn't account for edges, targets, etc. I just divided the area of the wafer by the sensor area). If yields drop for the FF (yields decline more for larger die) and the yield works out to even 4 to 1, then you get about 50 FF and 200 Crop sensors per wafer. If you account for pixel density I would expect the yields to even out (smaller feature sizes would see lower yields). So I think I am being somewhat biased in favor of crops here.
I'm not sure that smaller feature sizes are likely to really reduce the yield that much, i suspect fixed defects on the wafer are more likely and i think your yield calculations sound reasonable (though it's anyone's guess how many of those defects really exist).
I suspect the features on the 5D3 and 7D sensors will probably be quite similarly sized. Just because the photosites are larger doesn't mean you can afford to make the other circuitry larger.
It depends more on economies of scale than anything else, I suspect Canon can probably sell 10x the number of crop sensors so that drives their price down more. It'll be interesting to see if they make a low MP full frame rebel. I've always wondered how many potential 5d sensors are rejected just because they have too many photosite defects. Perhaps with some clever mapping and downsampling they could be reworked to make a rebel sensor