Sadly this is a python issue. They have the same problem.
Yeah, I see your point. I was reading more about py2exe to see what insight could be gain from it and they had this link: http://www.py2exe.org/index.cgi/PathModul . That is the same solution, manually changing import names, that we are looking at right now. However, their problem with external libraries is not nearly as bad as Constructs (mostly because it is all Python at first . For example, I was able to easily create a standalone .exe using the AIML libraries. I just can't do the same in Construct (even after lots of renaming).
So far the solution is to run an unofficial script that reads the libraries, creates dependency data and bundles everything into an .exe, option that is not useful for Construct.
That is true that py2exe (or pyinstaller) isn't immediately useful to Construct, but it seems entirely plausible that that functionality could be added to Construct with a lot of effort. However, sadly I personally don't think it is worth the effort considering all of the other bug fixes and updates that could solved with the time. I think I've finally resigned that it just isn't worth it to try to officially support other python libraries.