The University of Crete at Rethymnon (where we are holding the meeting) has a Guest House we can book. If you are interested in this please let Emma know (firstname.lastname@example.org). There are about 10 or 11 rooms, one of which has a wonderful view to the sea but is rather noisy). The bathroom facilities are very basic, but en suite and clean. Price 26 euros for a single, with breakfast. Double is around 35, I think, but rooms have only double beds (no twins)
Hotel Ideon is right next to the guest house, more luxurious, quite nice, with a swimming pool, on the waterfront but not on the part where you can swim. In the past Chloe, who is working with us from the University, has organized successful events combining the two venues, since that gave people a way to spend more time together (the guest house also has a lovely seminar room which anybody can use).
Prices for very few rooms that are left (no sea view, but this means they will be more quiet) is 67 for the single and 92 for the double, with a 10% discount, when you mention that you are coming for a University event: email@example.com. Also this is right next to the old town, so people can hang out without having to use cars or buses. Public transportation to the University is very easy.
Prices in euros, provided you book directly with them (needless to say). https://www.facebook.com/ideonhotel/
There is also the option of the big hotels by the sea, the disadvantage there being that you have to use a car to go back and forth to the town.
Or you could try airbnb