Don't forget that these auxiliary files are necessary for cross-referencing, producing the table of contents, index, etc.

If you are producing documents that don't require any of those, then this ought to work.

Also, instead of replacing the standard pdflatex, it is better to make it an alternative "Engine", using this nice feature of TeXShop.

Save your script in ~/Library/TeXShop/Engines, as, say,
mypdflatex.engine, and don't forget to make it executable.
(Also, add the line
#!/usr/bin/python
at the top have python run the script when it's invoked)

Then you can access your engine as you would any other engine, like xetex, of latexmk, or whatever. You can select it from either the popup menu or include the line

%!TEX TS-program = mypdflatex

at the top of any tex file to have TeXShop compile it using your script.

---
Luís

Don't forget that these auxiliary files are necessary for cross-referencing, producing the table of contents, index, etc.

I believe that when you set the output-directory, it will also look there for the auxiliary files.

And where can I set this Output-Directory?

The script does that for you.