How do you use the Apache "ScriptInterpreterSource Registry-Strict" directive?
It sounds like the ScriptInterpreterSource line is being ignored. If it's set to Registry or Registry-Strict, it should ignore the shebang lines and use the registry only.
Also, the Apache 2.2 docs have a slightly different location for the registry key:
HKEY_CLASSES_ROOT\.cgi\Shell\ExecCGI\Command\(Default) => C:\Perl\bin\perl.exe -wT
This works for Python scripts as well. I did the following to fix my Apache install to ignore the shebang requirement in my scripts. Without this the shebang is required in the current version of Apache 2.4 - or at least it was in mine.
# tell apache to use registry - this requried a registry hack
# to the following:
# [HKEY_CLASSES_ROOT\.py\Shell\ExecCGI\Command] = "c:\\python\\python.exe"
ScriptInterpreterSource Registry-Strict