Because clicking on it is the easiest way to get to the b.p.o home, and I would prefer to leave it that way.

I agree though that the Python logo might lead user to think the logo links to w.p.o, and afaict there's no direct link to w.p.o.
Two things could be done:
 1) add a link to w.p.o somewhere (e.g. at the top of the sidebar);
 2) use a b.p.o-specific logo  (writing "Issues" somewhere in the current logo might be enough);