Comments order is managed in plone.app.layout.viewlets.comment
:
http://dev.plone.org/plone/browser/plone.app.layout/trunk/plone/app/layout/viewlets/comments.py#L28
If you want to re-sort the comments you should override or change the original behavior of getRs
method. The final implementation depends on what do you want to do with replies to last comment.
Do you want replies to be also re-sorted? If so, I think that just changing the sort function should work:
rs.sort(lambda x, y: cmp(y.modified(), x.modified()))
Do you want replies to keep original sort? In that case, you should code a little more.