Oh wow, that's a lot of changes...!
Basically what I've got is a number of custom templates, which live outside the theme directory and get invoked by a template_redirect action. This is so I can support them across multiple themes, which I often use for testing/development - i.e. whether I'm using suffusion or something else, the active theme always references the same PHP templates (because they sit outside of each individual theme's directory).
Some of the templates use 2 sidebars and some use none. For simpler themes, omitting a call to get_sidebar() was sufficient, but I found that with Suffusion I also needed to explicitly set $suf_sidebar_count = 0 before calling get_header() to suppress sidebar rendering. Since upgrading to 3.6.5, however, this no longer works.
(I think you got that already, just wanted to reiterate to make sure.)
So, I'm not sure exactly what's changed, but is the only way to achieve this functionality now to edit the theme's source? If that's the case, it *may* just payoff to stick with 3.5.7, as my main motivation for upgrading was to eliminate my last core-theme-edit, the aforementioned "featured content hack." It seems like achieving the no-sidebar functionality in my custom templates now requires substantially more core hacks than this - unless there's still another way around to accomplish this directly from the template in question.
For reference, an example of a "sidebarless" template:http://www.justin-klein.com/potd/07_04_ ... _dsc_06_54
Whereas the majority of the pages use 2 sidebars, as per the suffusion options:http://www.justin-klein.com/