but that they didn't really kick off much discussion

Any idea why not? Also, could be that the book version will increase interest. It could also be that we'll get an influx of new readers with the book's publication and HPMOR's conclusion, so that might help.

If I know that somebody had an insightful response to a question discussing a particular article, I can't just look in the comments of that article--I also need to check out the rerun page, and now I would also need to check out the book discussion page.

Encouraging people to link / quote insightful previous comments might mitigate this issue, at least somewhat. Also, the focus of the reading group would be mostly towards newer readers, so we wouldn't necessarily be aiming for super-high-value comments. That's not to say that people won't have important things to say, just that it's of secondary importance here.

I expect we're better off having a sidebar link to the book reading group article of the day/week/etc.

From what I've seen about the glacial pace of edits to site mechanics, this is almost certainly not going to happen. Unless you know of an easy way to do it?

and encouraging people to post on old articles

Having a sidebar will make for extremely low visibility, and I'm not sure exactly how to encourage people other than that.