if you put just the guy in a separate render layer you shouldn't need to hide anything... choosing the render layer you put him in usually makes everything else invisible in your viewport automatically... and hiding things is probably what is preventing you from getting the proper render.

enhzflep: yea AE can do it, and pretty easily too. when you import footage files it asks you how to treat the alpha each time. you can ignore it, treat it as normal, treat it as pre-multiplied, etc.