Ah, you see I agree with Toynbee about the atmosphere - this week's headlines have dramatically underlined that. AND I agree that Jo's murder wasn't about Brexit itself.
That's because, significant though Brexit is as an economic event, I believe for some people it's really just the McGuffin. The plot device. The rallying point.
The US doesn't have Brexit, but they're having exactly the same type of politics emerging right now.
So I didn't read Toynbee as primarily writing about Brexit but bringing in Jo Cox. I read her as primarily writing about the much larger issue of this dangerous political trend, and pointing to stuff being hatched under cover of the leave campaign. (Though of course I'm not Toynbee, so can't speak to her true intention.)
I DON'T think you have to be racist to have voted Leave, or homophobic, or anti the rule of law. And I see the Trump-alikes, who seek disruption to give themselves a shot at power, as having found fertile ground in the Brexit campaign; rather than their behaviour being a true expression of everyone who voted Leave.
So the us-and-them I see here is between people who support parliamentary democracy, the rule of law, tolerance (the things nebulously touted as "British values"), and people trying to undermine those. Not Remain vs Leave.
Though the Wail are certainly trying quite hard to co-opt Leavers to their campaign of disruption.