Well, let's try that out on other statements where the belief is that the thing is (1) a choice, or at least suppressible, at least with education, and (2) bad.
"Racism must be eradicated from public life." Call for violence and genocide against racists? Not so clear, is it?
"Gambling must be eradicated from public life." Call for violence against gamblers? Not so clear.
"Cocaine must be eradicated from public life." Call for violence against cocaine dealers or users? Well...perhaps.
"Public flogging of women must be eradicated from public life." Fortunately, public flogging of women is already not a thing in most of the world, but is this calling for genocide on floggers and/or flogging-supporters?
Now, I would readily agree that all of these statements--and Knowles'--may engender violence. Strident words like "must be eradicated" suggest that extreme measures may be justified--maybe even violence. But it isn't a call for violence. And it certainly isn't a call for genocide.
Knowles is very clear in the clip that his call is to re-educate deluded people, which is what he thinks transgender people are, not commit violence. (He also gives plenty of wiggle-room to those who would commit violence to excuse themselves by using the etymology of instead of the definition of "genocide". He's playing with fire, and that deserves some pretty harsh criticism.)
Knowles is the deluded one (or plays at delusion to appeal to his audience). But that doesn't mean that he, and those who think similarly, are genocidal. And it also doesn't mean that those who oppose him have the right to engage in extreme violence themselves which would be justified were he engaged in actual genocide (and might be justified if he were calling for genocide and it seemed like it was working).
The way to counter people like Knowles is to point out where he's wrong. He's pretty darn wrong, so this shouldn't be terribly hard.