There have been problems in the past with releasing only source code, since the judges have had mixed success with compilation. An executable for windows will cover most of the judges though.
You could submit it within the time frame as source with compile instructions, then spend a few days after the jam finishes to create the packages you want. It's completely acceptable to spend time after the close for things like that. But people will want to play the game, and the first couple weeks after the jam will have the most traffic, so you'd want something playable by non-developers at that point.