Since a color filter reduces the range of visibility, it'd normally be monstrously stupid, but it doesn't end up impacting this particular manga too much. This is because the author tends towards darker shades of grayscale (i.e. the blacks are heavily distinct).
I don't think it adds anything either, though, despite not detracting much.
I'm happy with whatever the translators decide going forward, personally. If people want to manually readd the sepia, there's probably ways to do that with Chrome extensions.
It's kind of a crappy situation because there are clearly a lot of people who prefer the filter, but while it's easy for a reader to add, it's hard to remove if you wanted it removed. Since the amount of people who want it removed is apparently so small (and/or not very vocal), this is less of an issue though.