I've been to Santorini 3 times over the last 20 years, and would recommend that you keep your original plans. Yes, it has become somewhat chaotic, mostly caused by the cruise ships. Once the cruise hordes depart, Fira and Oia become very charming. That you are going in a shoulder season also helps.
On all three visits, I have done the hike from Fira to Oia. It is one of my favorite hikes and I have hiked throughout Europe. Last time I hiked it was in 2014, and it took about 4-5 hours. Make sure you have good and comfortable hiking boots/shoes, as you will need it. Even though the cruise hordes will be gone at sunset, it is also worth it to see the sunset at Oia. It is a little overrated, but it is very lovely. Here are three photos I took at sunset last time I was there.
Another worthwhile activity would be to visit the ancient city of Akrotiri, which is on the other end of the island. This is a major excavation site of the city that was buried by the huge volcanic explosion. Last time I was there parts of it were closed due to lack of funding, but I believe it is all opened now. And if I recall correctly, there is a black sand beach not far from Akrotiri. Take one day and do both.
I have also been to Naxos twice. It is very charming, and will offer you a calmer experience than Santorini. There are some hiking trails there, and they have a vibrant Taverna scene with great seafood, pasta etc.