Honestly, I was rooting for Mutagen Man to become a hero in some way (love the design, and I'm cool with underdog stories), and even as it stands I don't want to see him destroyed - but if it happens, it's out of the Turtles control.
The guy can hurl cars, tear down buildings, throw acid out of his hands and has zero understanding of right and wrong.
I see the comments saying "He was justified for attacking Raph and Mikey, and he didn't know any better."
He was going to KILL them -
REALLY, people gave Splinter crap for making them hand over their weapons - despite how easily they were able to adapt to that handicap.
But Timothy turns himself into Mutagen Man of his own free will, nearly shoves acid in Raphael's face, and vows to kill the turtles despite saving his life time and time again, when he was a human and even as an insane blob of guts. He even turned on Donnie, the closest thing he had to a friend who's been taking care of him and looking for a cure.
Mutagen Man get's a free pass because "It's not his fault, the mutagen made him do it." Or, "He never wanted to become this thing."
Well, to bad. He IS that thing now, and all he's doing is endangering lives. Had he become a "Cool" mutant and still ended up becoming a villain, would it still be the mutagen's fault?
The complaints about April, "They saved her life multiple times! She can't be mean at them just because they played a hand in her father getting mutated! So ungrateful."
Meanwhile, "The turtles saved Timothy's life multiple times, but he can't help it that he wants to kill them for no reason other than to keep April to himself. It's the mutagen! They need to be nicer to him!"
Hell, he was going to kill Casey for no other reason that being with April.
Would he have done the same to her father if he was with her (mutated or not), other friends in school?
The turtles already have the foot and Kraang to worry about - not to mention any accidental results that come from the missing mutagen. The last thing they need on their plate is a walking emotional time bomb to endanger the city.