My upstairs wood floors are slightly darker then my main floor. It doesn't bother me a bit. The stairs are a little darker, and since they land on the wood upstairs, but on a tile front entry on the main level, it seemed best that the upstairs match the stairs - all while still working with the stained doors.

So, two things to think about - how will new stain color on the main floor work with present doors if they are also stained, and will the upstairs floor look OK where it meets the stairs. If the difference is not huge, it should be OK.

IMHO it shouldn't be a problem since you are not looking at them at the same time.