Companies don't "want" things. They do not have a single will. Companies are agglomerations of many humans, who have various wills and more importantly various incentives.
Same with "HR," and not only are there multiple people, in large enough companies, there are fairly disconnected teams that handle the various parts of HR, like sourcing candidates, making offers to candidates, supporting managers, handling accommodations and keeping the company on the right side of the law, overseeing budgets and headcount. (If it helps, consider engineering, and the statement, "If engineering didn't want to move their legacy services to public cloud, they would simply have not signed a services contract with this cloud vendor in the first place instead of wasting their money.")
It's entirely possible that every individual on the hiring side genuinely wanted (of their own will) to hire this person anyway, but none of them were the same people who handle working with existing employees, who are all more misanthropic, and they don't talk to each other. It's also possible, and quite a bit more likely, that every individual on the hiring side is incentivized to fill roles, not to retain (how do you give someone an OKR or performance bonus this year based on whether their hires are still around three years in the future, anyway?), and that every individual on the existing-employees side is incentivized to demonstrate that they aren't coddling low performers.
Being employed at a company is a business transaction. It's not cynical to ask what the involved people's financial incentives are and whether they line up with yours, any more than it's cynical to expect that McDonald's will refuse to negotiate on the price of a burger. Even if the employee is nice, they've got a job to do, and they may not be nice.