Predictably, Maher let Milo run rampant on his show because he agrees with him on two pet issues: "free speech" (even though the government isn't involved at all...) and religion.
I don't know if I *totally* agree that people like him can't be shut down and can only benefit from public appearances. I totally get not wanting to give him a venue, but I think it is possible to shut him down. However, even Wilmore missed the mark slightly.
The fact is, people like Milo thrive on getting under people's skin. When you tell someone like him to "go fuck yourself," he feels like he's won. He even admits to getting off on it, and claims a victory because, "TRIGGERED!!!" He can laugh and throw out his "liberal outrage" line, and those inclined to agree with him will just assume that the liberal doesn't have an actual rebuttal, whether true or not.
It's also hard to use his hypocrisy against him because he has zero fucking shame. He'll throw gays under the bus and admit he's a hypocrit when it comes to religion. You can point out that this shows a huge amount of intellectual dishonesty, but he'll just say "humans are hypocritical" and try to sidestep it.
He also does the Gish Gallup, throwing out so much bullshit at once and talking over people in order to dominate the conversation. This was how he rolled over Maher (though he didn't put up any real fight, because they're not his pet issues.) Perfect example was the trans people involved in sex crimes bit. You need to respond by:
1) Telling him to keep quiet because it's your time to respond. He often will talk over people when they're trying to carefully address his "points," bringing attention to himself and his shtick while distracting from the actual issue.
2) Pointing out that he gave no citation for his "undisputed" statistic of trans people perpetrating sex crimes, and that the opposite is actually true. Again, he brings up things and claims "fact" often, when he has zero claim to the word. The same goes for the "I only want to protect women and children!" line. This is another conservative bogeyman with zero grounding in reality. It's a made-up scenario that has almost no occurrences in reality. It's used to frame the majority as victims when in reality it's trans people that are attacked and have their rights continually marginalized.
Plus, by his own "logic," gay people shouldn't be allowed in public washrooms either. But, again, pointing out his hypocrisy will be met with a hand wave.
4) Also point out that the DSM-5 correctly reflect modern psychology's knowledge on transgenderism. "Gender dysphoria" is no longer a thing, just like being gay or bi is no longer seen as being a mental illness. He can deny it, but that is denying fucking fact at that point. He is literally denying an entire field's analysis of an issue of their expertise, resulting in a disgusting propagation of ignorance that is demonstrably affecting real people, not just hypothetical situations.
So it can be done, in my opinion. But you need to be prepared and willing to fight back in an effective manner, which Maher clearly was not. Hell, you can tell the audience was begging for it, because when Wilmore and the former spy pushed back at all, they roared.
But if you're just going to be a pushover and let Milo run over you because he gives you token compliments, then it's probably better you don't have him on at all.