I agree that commenting is painfully rare, and making it harder makes them rarer; clearly a bad development. However, writing the comment is only half the picture, and I think you're overlooking the positive effects of the change.
Like I said elsewhere, I'm a big fan of the new location. Old-style comments were practically invisible specifically because the sidebar scrolls independently. If a story has a description and tags, the comments disappear off the lower edge of the screen for me, at least (even now), so I have to go out of my way to read them. I rarely bothered doing that, and I'm sure a lot of people didn't either. The only time I myself commented on stories were when I had something to say.
Whereas if you're reading a story, you're scrolling down as a matter of course, so new-style comments appear pretty much automatically. And because they're more prominent in the site layout, users will see them more often, and if you see comments more often, you're more likely to post. Because even if the chapter itself didn't cause you to want to say something, a comment still might. (This could be improved even more by reducing the amount of space between the last sentence of the chapter and the first sentence of the first comment.)
I acknowledge the issue that writing-while-reading has been made harder, and it would be nice if a fix could be implemented. I (and others) suggested a second (small) comment box in the sidebar. But moving the comments back too seems to me very much throwing out the baby with the bathwater.