If the comments start out minimized, and you click to expand them, the ads are still right there to begin with.
Respectfully, I don't understand why this would be a "solution" when there was no problem beforehand. I understand the idea of letting people comment while still reading or while scrolling back, but it doesn't have to be all or nothing. There can just be a place to click to expand the comments as well as a place to click to pop them up in the sidebar. Flexibility won't hurt.
As is, it's just not taking advantage of available space. If you can use the full space for browsing and reading comments, which is certainly possible as it's the way it was, why force it to only be visible in squished format that makes it impossible to have as much comment material on the screen at a time?