Long term, his legacy will survive. The music will ultimately outlast all of this, and the current controversies will be at most asterisks on that legacy. He is, and will be remembered as, one of the true greats.
Short term, he's done tremendous damage to his reputation and career; he will continue to tour and sell albums, and the fan base will hold, but it will be smaller and more marginalized. The albums won't sell as much, fewer people will come, the occasional venue might decline to book him. And consider the impact of all of this on tour merchandise, a considerable source of income for any artist; right now, a lot of people would not want to wear a Morrissey shirt in public, even if they stay in the fold as fans. The damage is real and will take years to recover from. He's 60 and doesn't have decades ahead of him, either. He needs to do serious work now to refocus public attention on his music and not on For Britain and Brexit and all of this political bullshit.