Hm… In more pure sense of the question I suppose you could filter active_plugins option on retrieval via option_active_plugins filter and throw plugin out for one of the sites. But I won’t try to predict what this can cause to active/inactive state in your situation. 🙂
I think more practical solution would be to figure out functions and hooks that SEO plugin uses and unhook them. Hopefully plugin you use is coded decently enough for that to be possible without much trouble.
One more idea – dump plugin in mu-plugins for one of the sites so it is forcefully active for it.