I would suggest upgrading ecommerce (and posting upgrades to bugtracker) as well as customizing.
The whole registration section of ecommerce can be removed fairly easily (for instance, see https://openacs.org/bugtracker/openacs/com/ecommerce/bug?bug%5fnumber=1072).
We've also disgarded the ecommerce user classes to use the groups in the toolkit as well (by changing the two tables to views with the same name).
The nice thing about ecommerce (and other existing packages) is that they are highly customizable and you don't have to start from scratch (like, for one project I stripped the ecommerce checkout to 3 steps). I think it's the easier route for you to go.
Good luck!
