Assuming for a moment that these registrations are real, and that the final title will definitely be one of these six, I think "City of Gods" is still the only reasonable choice. Here's my take:
1. Past IJ titles have a certain "flow" to them (ignoring, for a moment, the renaming of "Raiders" in the DVD set). They're short, and sort of roll of the tongue, so I think that counts out the longer titles like "Kingdom of the Crystal Skulls" and "Fourth Corner of the Earth".
2. "Lost City of Gold" is too generic, and as others have said it conjures up disturbing images of that wretched Alan Quartermain film.
3. "Quest for the Covenant" is there, I think, because of all the rumors going around about the Ark returning. It also makes the film sound like a "Raiders" rehash, which wouldn't be good for marketing. I would think they'd want the title to refer to something new and mysterious.
4. "Destroyer of Worlds" is too dark. I think the concept of family is going to be one of the focuses of the film, and the tone will likely be lighter, like Last Crusade. If that's the case, this title wouldn't fit with that approach.
5. "City of Gods" has that "flow" I mentioned earlier. It also refers to something new, but is ambiguous enough to keep you wondering about what that is. Plus, it mirrors "Temple of Doom" in style, which helps it to fit in with the rest of the series.
These are just my opinions, of course. The real answer will probably turn out to be "none of the above".