Unfortunately the reality is that a double digit percentage of all sites rely on document.write [1]. Whilst it's true that a lot of usage is advertising, it's also used for functionality in sites like Google Docs. Perhaps with a lot of work you could get the usage down to single-digit percentage figures, but disabling it entirely is going to break an awful lot of sites that are unmaintained. For something like NPAPI, where there is a real ongoing cost of support, breaking old content — with a multi year timeline for migration — might be worthwhile, but I think it's hard to make the case that document.write is in the same category. Yes, it's an old and terrible API that causes layering violations, makes writing scripted parsers much harder, and ideally authors would avoid it. But making it go away would be a huge project with relatively low payoff compared to other possible uses of the same effort.

[1] https://discuss.httparchive.org/t/how-and-where-is-document-...