You could perhaps partially obfuscate the code. But it'd probably be tricky to ensure that at least some interesting parts remain untouched. Perhaps let the template author markup those areas?
Meh. I'd say don't bother to obfuscate it. There's a real cost, and no obvious benefit (anyone making a real site would be stupid to steal their theme; anyone interested in stealing would just steal from a theme purchaser's site instead of you if you obfuscated).
From a dev's POV - I won't believe you on the elegance & quality of the source unless I can see it, and that's very much what I'd be interested in paying for (an elegant/clean/flexible UI base). Obfuscating at all is somewhat like selling a fabulous custom car but hauling a dirty tarp over it before letting the prospective buyer get a closer look.
Besides, it's HTML & CSS. De-obfuscating (unless it's seriously mangled, which seems dangerous) is as easy as copying the DOM and composed CSS from Firebug, I imagine, or cut/pasting the files into a good editor and auto-formatting.
Or something; I can't say I've ever de-obfuscated a webpage before; when I check the source, if it's crap I don't keep reading. Which may be part of the point, here.
If it were to be done that might be the only way to do it. The author is going to have a better idea of what they feel is the meat and potatoes than I would.
