I just tried using script_helper in a new test, so I have a couple of comments.

I don't see stdout and stderr being conflated, it looks to me like they are returned separately, at least by the assert methods.

The assert methods return results, which is unlike other assert methods.  This is very useful, even essential, and I wouldn't want to give it up.  That conflicts with the current unittest conventions, though.

It would be a big help if 'err' were returned with the refcount line removed if it is there, which would make tests using the methods return the same 'err' regardless of whether they are run under a debug build or not.

I think the names of the two assert functions should follow the current unit test conventions (assertPythonRunOK and asssertPythonRunNotOK, perhaps?)