Hi eoc;
Just did a quick test with default Autoptimize and Disqus settings (so no specific exclusions for Disqus in AO) and (at first sight) everything seems to work, cfr http://futtta.be/wordpress/blog/2013/07/12/autoptimize-disqus-test-for-eoc/
If it does not work, I would activate "look only for JS in head" in AO and "Output JavaScript in footer" in the Disqus plugin settings (which are hard to find). The combination of these should allow Disqus to remain unaltered by AO.
hope this helps,
frank