If you built
vim against Qt rather than GTK+ and
python-complete still isn't working, that suggests the problem isn't actually a consequence of trying to link to both GTK+2 and GTK+3.
However, since you haven't yet provided any details about how you built with Qt (Qt isn't officially supported, so you must have used a third party derivative of
vim), and you haven't provided any detailed information about what error messages or malfunctions you're having with
python-complete, it's not really possible to tell you how to fix the problem and get
vim working with Qt.
vim officially supports some GUI's other than GTK+ and Qt, and one such build is officially packaged for Ubuntu.
Just install the Athena version of
vim, which is provided by the vim-athena package.
You can install by clicking the package link above, or searching for it in the Software Center or Synaptic Package Manager, or running these commands:
sudo apt-get update
sudo apt-get install vim-athena
vim-athena doesn't depend on or use any version of GTK+. If you use
sudo apt-get build-dep vim-athena, it probably will install GTK+ and GNOME related libraries, because the
vim-athena binary package is built from the same source package as
vim and other
vim-providing packages. In any case, you shouldn't need to build from source, as the binaries provided by
vim-athena are already built against Athena and not against GTK+ or other graphical toolkits.