The Whisperers are defeated through a combination of strategic planning and teamwork by the main characters. They outsmart and overpower the Whisperers in several key confrontations.
Sure, Negan gets into conflicts with the Whisperers. Their encounters add a lot of tension and drama to the comic series. The battles are intense and have major implications for the plot.
Negan doesn't become a part of the Whisperers in the comics. The comic plotlines keep them distinct, with Negan having his own adventures and conflicts that don't involve the Whisperers.