In her new post on Monday, Rowling wrote: "I'm not owed eternal agreement from any actor who once played a character I created. The idea is as ludicrous as me checking with the boss I had when I was twenty-one for what opinions I should hold these days."
She said it had been, however, "hard to shake a certain protectiveness" after knowing someone since they were 10.
"Until quite recently, I hadn't managed to throw off the memory of children who needed to be gently coaxed through their dialogue in a big scary film studio."
The author said the "turning point" in her feelings came in 2022 when Watson appeared to aim a subtle dig at Rowling on stage at the Bafta Awards.
Host Rebel Wilson introduced Watson by saying: "She's proud to call herself a feminist, but we all know she's a witch." Watson responded that she was "here for ALL of the witches".
Rowling said that moment had "a postscript that hurt far more than the speech itself", when Watson sent a note, despite having her phone number. The note had a single line saying, "I'm so sorry for what you're going through", Rowling said.
"This was back when the death, rape and torture threats against me were at their peak, at a time when my personal security measures had had to be tightened considerably and I was constantly worried for my family's safety," the author said.
"Emma had just publicly poured more petrol on the flames, yet thought a one line expression of concern from her would reassure me of her fundamental sympathy and kindness."