I honestly don't think Apple's goons are sitting up in their ivory tower debating new ways to screw over consumers with pointless draconian rules. I'm sure that in principle they couldn't care less if users were keen on installing a TMNT theme, or a random fractals theme, or whatever else.
I think it comes down to security and privacy concerns. Theming requires modifications to parts of the iPhone which are not constrained to a controlled sandbox environment. If Apple were hosting something which was disguised as a cool new theme but which actually contained a malicious Trojan that stole your personal information, they'd share some of the liability for it. It's safer for them if they don't get into the theming business at all.
As has already been noted, with jailbreaking and a little creativity, you can create your own themes if you have the skill and inclination to do so. So it *is* possible to have it both ways. Hopefully, Apple will never seal up every possible method of jailbreaking.
