Your basic approach looks sensible to me.

One trick I use in test_cmd_line_script to prevent recreation is to simply delete the source file. If the source is gone, implicit recreation is impossible. Unfortunately, that doesn't work for __pycache__, since the cached version will be ignored if the original goes missing.

One useful explicit check (as per #14443) would be to ensure the magic number and other attributes are as expected:
http://hg.python.org/cpython/file/57d558f1904d/Lib/importlib/_bootstrap.py#l444

You can also pass the "-B" flag to your testing subprocesses, which will switch off the implicit bytecode generation.