Yes, it's usually best to keep compiled files out of version control unless you have a specific reason for doing otherwise. Most IDEs will generate seperate src and bin folders which makes this easy enough. Just initialise the repo in the src folder and it will have no knowledge that the compiled files exist.

Phrased another way, if compiled languages were indeed incompatible with source control then that would be a reason for discounting doing serious development in compiled languages altogether.

You can also point out that git was designed specifically for use in a compiled project (the linux kernel).