This question has been asked a few times already. Kongregate provides support for web-playable formats, which doesn’t include exe yet (maybe native client?). In order to upload a game on Kongregate you need to use one of these formats. Supported files/software that I am aware of are: Flash, Unity, Java, HTML5, and Silverlight.
I do not believe there will be any plans to change this in the near future. The biggest hope for games written in C/C++ is the Native API (which is not the same as Native Client as mentioned earlier in this post), which is reserved for high quality desktop games.