Well of course that will have to be my only option soon, but I think it'll only be more inaccurate to get rid of them. First off I'm using a population database as Exile does, so all the cities do have completely accurate populations, and obviously the Asian cities are individually larger than those in Europe so the populations are accurately represented. For instance, many cities in Europe would have populations of 5 to 10, while Asian cities are consistently from 15 to 35.
The reason Europe is so crowded is just a usual problem with making a global map, where Europe's density of population is hard to recreate as the map of Europe is so much smaller than usual. The density is there to demonstrate the difficulty involved in conquering Europe, to simply recreate density better, and to recreate the region's industrial strength compared to other areas, whether dense or not.
If there truly is no way to change the limit (responses to my thread have informed me that there is a technical reason that it cannot be hex-edited, after many many many tries by some of the best hex-editors here), then indeed I will have to spread out the cities to what I find to be an unrealistic point.