An easy solution is to put suffixes behind city names, that point to the civ's language. For example, in (East) India many cities have suffixes as -nagar, -abad or -pur which mean simply -town as in Jamestown or Louisville respectivly. So Hyderabad means Hyder's town. Same with Persian: -abad and -pur are originally Persian words, so there is Nishapur. In Arabic you could put an article before the name, as in al-Qahira. In German you could use -burg, -hausen, -heim and so on.
So if the Indians controlled Houston it could be Houstonabad or Houstonabad. There could be a Bataviaheim or an al-Chikagu. Not necessarily historical but closer to the flavor...