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It all depends on your campaign's notion of the power scale, really. Old-school D&D was a lot like Greek mythology, assuming that powerful mortals (level 14-20 or so) could challenge gods directly. Nowadays, most campaign settings have numerous high-level NPCs as fixtures of the world - for example, the king of a country being 15th level, and served by underlings of levels up to 12.
Personally, I favor the former interpretation. A lot of traditional storylines have difficulty maintaining verisimilitude if NPCs over level 6 are common... mostly because certain high-level spells have far-reaching consequences. The downside is that popular monsters like balors, solars, and the like make little sense if interpreted as followers of a deity. Dragons of sufficient age would also become tantamount to gods in their own right.
Personally, if trying to make a capstone encounter with a deity, I'd give them freeform abilities not easily converted into measurable statistics or challenge rating - make players think of solutions outside the normal combat "box." For example...
The benefit is that the combat is meaningfully different, at least in some small way, than just beating on the deity with sword and spell until it inevitably succumbs like any other entity. This is a pretty similar idea to 3.5 Loyalist's mention of everything having a weakness. In this case, I think style should dictate that the weakness is actually the downside of some phenomenal cosmic power tied to the deity's portfolio. A god of might could be ponderously slow, for example, or a god of nature could be poisoned by the merest touch of an alloyed or forged metal. Try to think of extremes of ability or spirituality that would be a double-edged sword to actually possess.