Probably I'd try to fold the second site into the first branded domain as aakk9999 describes, but keep in mind that 301 redirects are likely also to redirect any backlink penalties. Tradeoffs between preservation of the domain, preservation of the brand name, the pain of disavow, traffic redirection, etc, need to be considered.
Sounds like the company has been around long enough that its branded identity is likely to be worth preserving. That said, the WordPress themes are a major transgression, with unmistakable intent to spam... and, as you notice, they tend to be hard to get rid of.
See this discussion, which as I remember occurred before the disavow tool became available...
Google wants me to remove links from sponsored WordPress themes http://www.webmasterworld.com/google/4445558.htm [webmasterworld.com]
My guess is that to demonstrate sufficient penance in your reconsideration request, so Google is reasonably sure that this won't happen again, you may have to go so far as to make available an unlinked version of the theme and perhaps offer it to the domains now using it as an "upgrade", and to document those offers carefully.
Backlinks from themes to inner pages could be removed by dropping those pages. Theme links to branded home page, though, may or may not be disavowable if they continue to pop up. So the price of keeping the branded domain may be constant monitoring and disavowal of new uses of the theme.
To simplify the task, I would consider using some kind of blocked redirect page to redirect traffic-only from the second "seo" domain to the branded domain. See this discussion...
Best Way To Redirect Home Page Without Forwarding Penalty / Penguin http://www.webmasterworld.com/google/4606464.htm [webmasterworld.com]
Ultimately, you'd be preserving the home page of the branded domain, and also the brand name.