Way before I did a factory reset, back under 2.1, I simply deleted all the contacts on VZW's website, then opened contacts/menu/more/settings/and unchecked "phone contacts", leaving "Google" checked.
This should keep Backup Assistant out of harms way.
Since Froyo, things seemed to have changed a bit in that I sometimes find "phone contacts" to be automagically checked of it's own accord.
But, with no contacts on the VZW site, and refusing to allow Backup Assistant to activate, my google contacts have remained as I want them, not Moto.
YMMV ...