It doesn't even make sense for Kongregate to accept C source code
in the first place. Are you sure that's what they require?
A quick look at their FAQ gives me this: http://www.kongregate.com/pages/help#uploading-q-2
What format of games can I upload?
We support Flash (swf) files, HTML5, Java, and Unity game files. We do not have any plans to support executables (exe). We also support additional files through an iframe.
Additionally, games have a maximum file size of 20MB and a maximum width of 800 pixels. There's not a hard height limit but please keep it reasonable to make sure your game is still playable.