Paul Reubens was merely on sabbatical when the arrest occurred. CBS actually wanted another season. It is possible another season, maybe more, would have been produced. If the show wasn't a hit, they wouldn't have been showing reruns at all. CBS was hoping Paul would come back the next year.
ennobbe seems to have a different timeline for Pee Wee than actually occurred. Pee Wee had a big break in 1985 with the film Pee Wee's Big Adventure, and his Saturday morning show aired from 1986-1990. This is way past a "late 70's and early 80's but was already out of style". Pee Wee's Playhouse was a huge hit - and it wasn't just a kid's show. Many teens and older audience watched it too. It was a cult persona - something many others liked besides kids.
I do agree that Pee Wee as a character had a limited shelf life, but Paul Reuebens likely had a few more years out of it if he wanted. However, I think he was getting tired of the role and was looking to do something else. Whether he succeeded as a straight actor, or succeeded in another persona is something impossible to predict. However, coming out of 1990, Paul/Pee Wee had a very hot career. Everything would depend on the projects he picked. He did have one big supporter though - Tim Burton's directing career was about to take off. It's possible instead of using Johnny Depp exclusively, he might use Paul Reubens a lot as well.