A lot of RPGs do have those undertones.

Quote Originally Posted by the grand list of console role playing game cliches #89
Well, That About Wraps It Up For God
All major deities, assuming they actually exist and weren't just made up by the Church to delude its followers, are in reality malevolent and will have to be destroyed. The only exception to this rule is the four nature spirits who have preserved the land since time immemorial, but now due to the folly of mankind have lost virtually all of their power and need you to accomplish some ludicrous task to save them.
But FF games really don't do that as much as other RPGs. At least not any FF games I can think of off the top of my head (granted I'm not giving it a lot of thought right now). That is, unless you count the Final Fantasy Legend series for gameboy, in number one your party decides to kill God at the end for no apparent reason. Really the perfect end to a game that feels like being on an acid trip to begin with. Not that I know what that's like.