"will prefer" is not correct because the paving has already been completed and the dirt roads can no longer be preserved.
"would prefer" is closer but does not quite work because, again, it is no longer possible to preserve the dirt roads (they could be replaced at this point, but not preserved).
You could say "...who would have preferred that the dirt roads be preserved."
There are other possibilities as well. For instance, you could change the sentence to something like this:
"Although every road in the town is now paved, there are actually some residents who wanted the dirt roads to be preserved."
You could also tighten up the sentence a bit by saying "...paved, some residents had actually wanted the dirt roads to be preserved."