So I want to join a game jam and the only way I can see how I could do it is by using Scratch, a visual programming language. Now someone has made a scratch to swf. I can also convert swf to exe but it clearly shows it's using flash.

My point is, could I submit a game like this?

Why not, unless the jam rules include explicit format requirements. Any way you can make a game is fine if people can play it and have fun. Don't be ashamed of your skills, whatever they are!