Afternoon Rui;
On my test-instance I have Disqus working without any special configuration in Autoptimize (no need to have AO preserve HTML-comments), but there might be some other things going on. I would suggest to have a look at the FAQ for info on troubleshooting.
My best guess; there are JS-errors due to optimization that impact Disqus. Look at your browsers error console to get an indication of what to exclude from optimization and adapt your AO config accordingly.
Good luck!
frank