There is no evidence to support this.
One can't prove a negative, but no evidence has been found to support this. The description of Civilization V, taken straight from the official website, just states that the player is striving to become ruler of the world (and this description is no different than other board or computer games):
In Civilization® V, players strive to become Ruler of the World by establishing and leading a civilization from the dawn of man into the space age, waging war, conducting diplomacy, discovering new technologies, going head-to-head with some of history’s greatest leaders and building the most powerful empire the world has ever known.
There is nothing within the game that supports the theory that the player is actually supposed to be an alien. Not in the manual, not in the Civilopedia, and (as far as I know), nothing from the developers.
We have just as much proof (i.e. none) that Civilization V is:
- Machines running a computer simulation to keep humanity happy while they use them for batteries (The Matrix)
- A means of sending instructions to a planet of real people somewhere else in the galaxy (Stargate Atlantis, "The Game")
- A simulation of AIs, with a lone submarine located at the south pole observing everything and collecting the leaders of the fallen civilizations. (@CBredlow in the question comments)
- The collective consciousness of Sci-fi Stack Exchange users dreaming up an elaborate history of humanity