That is normally a slower time of the year, but I'd still guess there would be some crowds on the weekend days. And who knows what crowds will really look like this fall as new stay patterns may emerge.
As for whether you should pay extra over SFR to get EPs, I can't tell you what you should do. I can tell you that I have gone more than once over that time frame and almost always stay at a Premier hotel (to get those EPs.) So for me, the expense is worth it (of course that does depend on just how large the price difference is). It is great to be able to decide last minute which park, which rides, etc. and not have to worry about wait times or whether a particular park will be as crowded as another. It provides a very laid-back park experience.
For you, only you can say.