If your coworker is indeed a social troglodyte and you have documented cases of his hostility alongside your team's support, then your manager can cry all they want;
Paraphrasing a 2015 Harvard Business School (HBS) paper:
[...] toxic workers are so damaging to the bottom line that avoiding them or rooting them out delivers twice the value to a company that hiring a superstar performer does.
They are not an asset, they are a hindrance to your productivity and your manager ignores this. Contacting HR would be shooting themselves in the foot. Threatening to do so is incredibly petty, and in no way assists their incorporation into the team.
This behavior by your manager is nonsensical. If you don't mind me being skeptical, your manager might as well be close friends with this person and is turning a blind eye.
If you have no evidence, attempt incorporation and document all instances of hindrance that happen; file a complaint as soon as you can alongside your teammates because this sort of fiasco is not cheap.