Tholos may well be closed by then as they are in quite an exposed location and get nailed by the wind but if the Odyssey is still open I have heard that that is an affordable option for light meals in the Harani area, especially with Mike (ex Sunflower and Daphne's) doing the cooking
Mylopetra usually shuts early October. The Dolphin pizzeria is usually still open full time in October. Another place that is fun to go to when the weather is chilly is Haritomenos on the hill - they have a log fire in the dining room so if it is too cold to sit on the terrace (althought part of this is glassed in) there is always a cosy inside option.
as the Nireus restaurant is a 100 seater they are unlikely to keep it open once there is only a handful of guests in the hotel as the overheads would be prohibitive and they wouldn't have the stock turnover to justify offering a full menu. The smaller places frequented by the locals stay open longer as they are often small family run businesses and what isn't sold is eaten!
In places with traditional Greek menus it is customary to share dishes mezze style and as things like meatballs, tzatziki, Greek salad etc are usually only around 5 euros a plate it is quite easy to put together a very filling meal for 15-20 euros ahead including a carafe of house wine and a big bottle of water.