Sounds like you are trying hard to shot yourself and you will likely succeed. Every framework has its own assumptions and limitation so if the assumptions of wordpress do not fit your needs then just don’t use wordpress for the project.
If you (ok, probably the client) have decided that for reasons of cost, delivery time and maintainability wordpress should be used then you should strive to use the built-in wordpress tools instead of trying to go around them and re-inventing things just because if you were using framework X you would have done it that way. the more aligned you are with the wordpress core development practices the happier you will be (unless you are trying to ensure job security ;).
Sorry for the very meta answer but from your description it sounds like you don’t want to do this project in wordpress although I didn’t read here anything which might be problematic in wordpress and there is no need doing all the hacks that you think you should do.