I have read many posts about nefarious activities using high tax rates to grief the residents of the town before the company left for another server or faction.
In another game I played there was a cap on how much you could raise or lower a tax rate. I believe it was one tick per day. It would require a number of days to max out the tax rate. Tax rates were also based on the faction. You could raise or lower taxes for each faction as you saw fit. If you had an alliance with one you could lower the rate for them. You could lower the rate for all to entice people to use the town for crafting etc.
The towns also has regular elections of the governor. The towns were not owned by guilds or companies. This created some other less than desirable outcomes with cross-teamers getting their alts elected and trashing the town taxes etc.
I have not owned or been part of a company that owns a town so maybe there is they type of throttling already in the game.
Other than EF and the income does it really matter what faction you are in deciding where to have a home or trade from? It appears that factions are essentially ignored in towns. What if they were not. Would that create more desire for other factions to take a town?