I've actually tried that C64Studio. It seems pretty nice, if a little buggy (I emailed the author a couple of times)
But you can indeed take a BASIC PRG file from a D64, open up the basic code, and compile it to a new PRG file for reinsertion back into the D64.
The Import File... menu in the D64 window is missing a function call, but the author said you should be able to drag/drop the file in. Whether all that will work properly via Mono, I'm not sure though, didn't get that far with my testing