Is that Passenger doesn't honor the path or that the PATH isn't set up?  The files in /etc/profile.d/ are only executed for login shells, so you may need to modify your upstart script to either source that location or set PATH in there the same way rubber would.

Anyway, I'm not outright opposed to this, but I want to make sure this isn't a band-aid for another problem.  It's also a change I'd want to try out for a bit before releasing.