Why not just allow the taxes to be reduced and not increased for now? Lower taxes would bring more business possibly generating better profits in the long run compared to the normal price rates. This would maintain a small incentitive for city control for now without affecting newbies and adding the obvious exploitation of raising them above the normal price ratio.
We actually came to this conclusion also, however we want to replace the tax rate system with something that gives players a reason to strive for town control a week from now, 6 months from now and a year from now. There are some serious issues to deal with should you allow a universal discount for prices in a town, and we want to make sure no exploits slip through the cracks. Hopefully soon we will have the systems in place and will have an open forum discussion on additional ideas for faction town control.