I know it is probably not a popular move, but I disable Ancient ruins for my games at Emperor with the rationale being that the computer starts with more units, is likely to explore the map faster, and thus likely to gain more benefit from them. There are few things more disheartening than getting a great start in the desert with incense and being unable to get either desert folklore or the +1 culture/+1 faith pantheons, simply because the computer is exploring like mad and getting free faith from ancient ruins.
That logic could be applied only if the AI was smart enough for this to matter. If you get 2 decent ancient ruins, and each AI get 5, you'd actually be ahead .... The thing is, that on emperor you can get a lot more than two, but as in all levels you have to start with at least 2 scouts ...
And Incense is the last thing you'd want from a desert start. Desert Incense tiles are just worthless until the very end of the game. And also, by the time you can get faith from a ruin (thats available past T20 on standart), most ruins should be gone anyway, so I don't really see how that matters for the pantheon ...