I think it's fairly clear at this point that they are attempting to make it from the ground up, given the way they're handling it and the fact that "rebirth" was in the promo image. Many portions of the REmake do appear to have been recreated for the HD release and its in the context of recent upgrades of those two GC games that this is been planned. There has to have been a moment within Capcom where they said "you know what, we can actually do this."
Yes, everything would have to be made from the ground up, but RE2 isn't a terribly large game. They'll have to work on the city, the R.P.D., the sewers, and the lab. And then just all of the in between stuff or one new area, should they decide to add one in. It's the most popular game in the series outside of RE4. Maybe the combination of these two factors have justified it.