I can appreciate how some people would like to believe that Hunter had genuine enthusiasm for the show and that had circumstances been different he would have accepted the role of captain for the 2nd pilot. But I don't think it's really possible to truly know from what little we're given from the few sources available.
Hunter was in at least 2 productions that were published in 1967 following the 1st Star Trek pilot, with nothing noted in 1966. It's likely Hunter didn't have offers waiting for him at the time, but likely he was prospecting for other work. According to the 1994 authorized biography of Gene Roddenberry, Gene had written Hunter in April 1965 saying "I am told you have decided not to go ahead with Star Trek. This has to be your own decision, of course, and I must respect it. You may be certain I hold no grudge or ill feelings and expect to continue to reflect publicly and privately the high regard I learned for you during the production of our pilot."
I think we can agree there's a consensus that Gene did NOT drop Hunter as eluded to by the OP. Jeffrey decided not to sign up for the 2nd pilot, and it doesn't really matter if it was his idea or his wife's. Apparently he didn't disagree with his wife either, or he would have responded to Gene with reconsideration.
At the time, television programs weren't as highly regarded as movies, and certainly sci-fi was looked down upon as B-movie material (it is a far cry from how things are today). It's all about context. And frankly, if Hunter was keeping any tabs on Star Trek, by the start of the 3rd season seeing the show shelved into the "dead slot", he was probably thinking he made the right choice.