I think the biggest thing here is that you are saying that we don't need to boycott her work due to the fact that there are other interpretations of it. 

implying that Rowling's not-so-recent public persona saying a ton of 
wrong things destroys HP or automatically means that we ought to stop 
supporting their work is just as wrong.

I would say it's much worse to do things to support a person that has these views, by, for instance, paying for their media, than it is to alienate their media. Losing a bit of media can be sad but is quickly gotten over. Racism, antisemitism, and anti-trans stuff is not. 

JK Rowling's views can be completely separated from their work 

You can completely separate it from your own subjective standpoint, but with things like this, it's more important to as a society, in no way support people that have these stances. We should do everything we can to make these worldviews as unwelcome as possible. And I wouldn't say this is different whether that person is alive or dead. 

it's very hard to see a world where the impact of "boycotting" her actually matters

The effect, just like many other small choices we make on a day to day basis, is a larger and larger group of people speaking out against people like this. If you are willing to give up media due to how you feel about the creator, which is saying a lot for most people living in first world countries, then it's an idea that's everpresent in your mind, and in the minds of those around you. And that's powerful, in a positive way.

only really affects a small section of the population,

That is a terrible, and apologist view of it. Just because something terrible someone is doing is only effecting a select few people, that doesn't mean it's not wrong, nor does it mean it shouldn't be stopped. If someone had a specific serial killer criteria that only effected 0.0000001% of the population, they're still doing a horrible thing by killing those people, and especially when all you are talking about doing is to NOT consume their media or openly support them, it's really not a large price to pay. No discrimination towards any marginalized group should be tolerated, really ever.

"creator bad work bad" is not a good analysis of art

Sure, terrible people can create amazing things. Probably the most valid point you've had. That doesn't mean that consuming those things is worth supporting terrible people. 

you should not be guilt-tripping people into anything

With something like this, I agree. But that doesn't mean that the people who do the bad thing, are good. The only reason I'd say don't guilt trip people into it, is because that's manipulative, fucked up and, maybe, your judgement isn't perfect. But not because it's somehow acceptable to support a fucked up individual.