I managed to add filters for my custom post types with a few tweaks to the plugin code.
The basic process, for anyone who wants to do it on their own:
Modify sphinx.conf to include a new attribute, isForum (or whatever post type) and edit all four sql statements to query this post type.
Edit /wordpress-sphinx-plugin/php/sphinxsearch_frontend.php and mimic the structures used for comment/post/page/tag filtering. There are a handful of places this needs to be done.
Edit the widget/panel template files to include the appropriate checkboxes.
Obviously these changes will be lost on update, so right now I'll have to hand-merge updates. I'm going to try to write a few hooks that would make this a more generic process for others, if you're accepting mods to the plugin.