Living in a small college town, I am pretty sure I can assume that our models won't be replaced anytime soon. Maybe this is some good news for the geo-modeler community: if you concentrate on less-populated areas, then the chances that Google will replace your models with auto generated data is very slim. It is likely too cost prohibitive for them to fly over those areas. Having said that, it might be useful for Google to announce a population cutoff below which you guys will not cover cities - that would give modeled some certainty.
Another idea is to have a "geo-modeler" layer next to the new 3d buildings layer in GE. This could then feature user-generated content and could be turned on by the user, if desired. You could even implement it in a way where - when turned on - the new building mesh is not displayed where user-generated models exist. That should be easy to implement using bounding-box cropping.