Did you get any further on this? About a year ago, I took a look at Drupal 7 + Übercart, and the issue that you mention, was the showstopper: I couldn't get it to work, so I wend back to Drupal 6.
It's probably only of limited help, but maybe you find a useful module or hint among the documentation that I maintained at that time. Although in Dutch, you'll recognise the names of the modules: http://devliegendebrigade.nl/wiki/index.php/Importeren_van_artikelgegeve...
Please post a follow-up if you got it solved: I'm about to try Drupal 7 + Drupal Commerce, but only if I can indeed import hierarchical taxonomical data long with products.