This problem is caused by limited road information in OSM data which is used by MSFS. To create street lighting you just need to assign lighting to the different OSM street types. There are more than 10 oad types, so you can assign different lighting effects for different road types. Unfortunately the same road types can exist in urban and rural areas. In order to get around this you have to have some method of differentiating roads in rural vs urban areas. Unfortunately OSM data does not have enough information to make this distinction possible.
I did some scenery design for Aerofly FS2 using the same OSM data that MSFS uses and the only way to avoid this is to exclude rural roads manually. This is difficult even when doing small scenery areas and virtually impossible if you are designing scenery for the whole planet as MSFS does.
So lit roads in rural areas is just something you have to live with, until some bright spark comes up with a reliable method of identifying and then excluding rural roads en mass.