I think a good solution would be to have opinion pieces in another subdomain such as blogs.mynewspaper.com/ephraimgoldstein with a very different design from the rest of the paper.

Maybe. I'm saying more that there really isn't a problem on the paper's end.

The problem, if there exists one at all, is the reader ignoring words on the page of a publication that is expressly about transmitting words.

That said, the Guardian already uses a completely different highlight colour for its Opinion section than it uses for its News section.

Like the way editorials in print newspapers are always left justified (ragged right), while news articles are fully justified[0]. It's subtle, but for anyone who's been reading newspapers regularly, it's immediately obvious.

[0] At least, that's the case here in Canada.