Check out how DigitalOcean does this, on their tutorials. As you scroll down, a small box appears in the left margin asking you to sign up for the newsletter. It doesn't block any of the content and you can ignore it while you continue reading. That's nearly perfect, and an example of how to do it right.

I still find the animation of it appearing distracting and I think it interrupts the 'flow' of reading the article, but it was easy enough to block the element with my ad blocking extension.

As an aside, Firefox + Noscript are a thing of beauty. Using them I just don't see most of these annoyances. Yes, it 'breaks' many websites but this usually means a much faster page render without all the annoying stuff.