Manomio's C64 emulator wasn't refused for licensing reasons. It was refused because "an Application may not itself install or launch other executable code by any means." That means booting ROMs, which is the whole point.
Touch Arcade points out that "a number of apps in the App Store" already violate that provision, including:
[...]CHIP-8 emulators, programmable calculators and, of course, Frotz, a Z-machine interpreter. In fact, Sega's Golden Axe and Sonic iPhone games are nothing more than emulators packaged with the original game ROMs.
The app was denied last week; no word on what the next step is for the developers. But since they went to the trouble of signing a proper deal with the licence owners for the Commodore 64, it's a good bet they won't give up the first time they're told no.
Otherwise, there's always Cydia. Make it happen, guys. I dig that old school keyboard and Wico stick interface.
Here's a video of the emulator in action.