Yeah, can't really agree there. One of the things that Rowling did very well (all imo and ymmv, of course) was to illustrate the difference between someone being merely 'mean' and being 'evil'. Snape was mean, vindictive, grumpy etc, but we never saw him do anything evil- similarly, we saw Draco do a lot of 'mean' stuff but when he had the option to do something actually 'evil' he didn't. And Snape was counterspelling Quirrel as far back as the Philosopher's Stone. That isn't proof absolute of her always having a specific plan, but he was clearly always intended to be set up as an antagonist rather than a villain. It would be pretty difficult and almost certainly more clumsy to have set everything up in the first few books.
That is probably the biggest issue. Other similar(ish) series like Wheel of Time or Song of Ice and Fire use the same limited 3rd person perspective, but have multiple people's perspectives rather than one* which allows for more nuance; and whatever else HP is a ~teenage schoolboy. So in ASoIaF you start off with Jaime obviously being the bad guy (and he is one of course, he's just not the worst guy) because you see everything from Eddard's or Catelyn's perspective, but once you start getting Jaime's viewpoint you can at least understand him more. That isn't really an option available to Rowling even if she'd gone the multiple pov route due to Dumbledore and Snape simply knowing too much, but she does at least repeatedly have Dumbledore saying how much he trusts Snape, which is fairly close.
*I have noticed some people have difficulty with those perspectives clashing and thinking it makes the writing inconsistent; I've always kind of wondered if it's due to Harry Potter despite there clearly being times when Harry is wrong about something that he strongly believes via his own perspective.