The reason why it got cancelled is actually rather sad.
President of the network went on vacation. Turned over management duties to some young hot-shot. Wanting to impress the President, hot-shot decided to cancel a big show that was starting to struggle in the ratings. (No, not that one.) Hot-Shot cancelled Gunsmoke. Little problem.... The President of the network was literally the show's biggest fan. Oops! Needless to say, upon his return, he was furious!!! So, he immediately brought back the show. However, after it was cancelled, it's spot on the line-up had been filled. They needed an hour.
So, two half hour programs that were back-to-back got cancelled instead. That equaled an hour for Gunsmoke to be put back on the air. One of those was a half hour daily news broadcast. The other was Gilligan's Island.
Nevermind the fact that the show actually had darn good ratings at the time. Yes, it was doing well. But the President of the network actually hated the show. Kept it on the air due to the ratings and not having a reason to cancel it. Now all of a sudden, he had a personal reason.