A lot of people bonded closely with the Harry Potter series and it became a place of retreat and comfort for them. Having the author do things they see as wrong disrupts that familiar comfort and leads them to question themselves. That is what makes this so hard for them.

Lovecraft fans relate differently to his work. Rather than being a source of comfort, HPL's writings consist of a great collection of uncomfortable, existential ideas that the reader has to wrestle with, and appreciating them means entertaining feelings and beliefs that are dissonant with one's own. As such it feels natural for the author to be someone you wouldn't want to meet.

There is also the matter of pity. JKR has it all. Wealth, power, prestige. She's a rags-to-riches success story. Who pities Rowling? On the other hand, being Lovecraft is suffering. He was a harmless nobody who lived a short, miserable, lonely life. If you took Harry Potter away from Rowling she'd still be an aristocrat. Taking away Lovecraft's postmortem legacy just feels cruel because aside from a neat headstone it's literally all he's got.

And even Lovecraft got better.