It's not the quality of the accommodation that determines what you do with used toilet paper, it's the same all over the country. The reason is that a long time ago someone (I believe the English!) designed the disposal pipes too small, which means that if you flush the paper in the toilet bowl it causes blockages.
Whenever and wherever I've stayed in Greece, even in the cheapest accommodation (and I have stayed in some very cheap places) the bins are emptied daily, and in more upmarket accommodation (i.e. hotels) you get bins with lids (like Brabantia bins) so there's no odour.
Millions of tourists every year cope with this arangement, it really is no big deal. But, like I said before, if you feel you can't, there's no point stomping your foot and expect a whole country to change - just choose another destination for your holiday. God knows there are plenty of other places in the world that are worth visiting.