Hmm.. got point. I'd say you could:
1) Make lots of different tile sets and load the right one on demand
2) Make one tile set and apply a colour transformation on demand. See
here
3) Mask over the whole image. I don't quite see why the entities wouldn't be darker if it's night time. Unless you want dynamic torch effects. Which
wouldbe cool.
4) Blit and mask stuff under enities, blit enties, blit to buffer then mask, then blit stuff over enties. Does seem a little unnessersary. See
here
Zip