Maybe this was old 00's internet urban legend, but it is still mentioned on Malcolm in the Middle Wiki
But once upon a time a fan website stated:

Malcolm’s Original Finale

Malcolm fans will recall that the season ended with Dewey’s babysitter (Bea Arthur) being whisked away
in an ambulance to a hospital, (it was up to us, the viewers to assume she would be DOA).

But Bryan Cranston, (Hal), says that show creator and executive producer Linwood Boomer had other plans.

“Originally, Bea Arthur didn’t die,” he says. “She fell in love with Dewey so much
that she kidnaps him. (In the original script) they’re driving away, and Dewey has a black wig on and a
little black moustache and she says to him,

‘From now on, your name is Pepe.’

However, the finale was never given the green-light.

“Something about Maude abducting and seducing a little kid....”

        

Dedicated to http://www.angelfire.com/tv/reese/