Crete will be lovely at that time. When we were there a few years ago now( in July) we found Knossos very hot and there was little shade. Our guide told us at the time that it was nice to go through a tour without someone fainting! September should be much more pleasant. We spoke with people who had hired a car and they had no problems and enjoyed going off on their own and exploring.

we went 2nd and 3rd week last year and doing the same this year, the weather was great!!

Crete and the area you are staying in is fine in September. Its NOT the month for rain !!! and the temp less hot and more bearable. You will have a wonderful time. The Cretans are such a lovely people, friendly and welcoming. Yes there will be less crowds and a visit to Knossos is well worth it. Best time is late afternoon as there are less crowds then.
Rethmynon at night is to be recommended with a fish meal on the harbour, after walking the picturesqe narrow streets. Also dont forget Chania and its wonderful venitian influenced architecture and harbour.
I can also recommend a visit to Kalives a typical crete seaside village lived in all year. it will give you a flavour of real Cretan life. Also there are wonderful safe sandy beaches there too. If you want more info about this area Im happy to tell you more.
john