It's been done many times before, quite successfully. The Napier Deltic (3 crankshafts!) and Junkers Jumo are two examples. The Commer Knocker is another (which had only one crankshaft I believe). Two crankshafts makes the engine slightly taller, but not egregiously so.

I'd be curious to know more about the heat problem you've mentioned. Naively, there should be much less waste heat to dispose of due to the fact that the same cylinder volume is doing twice the work.