Totally disagree. For one, Civ takes way more thought and strategy. You are competing against something and must better your methods in order to win. For two, I know that in my own RTS playing time, I have to constantly and quickly calculate resources, allocate said resources, evaluate probabilities, problem solve for difficult defenses/offenses from my opponent, calculate build times and optimize efficiency of both production and damage output. I'll be the first to admit that nothing in this game makes me a mathematical/logical/tactical genius, but having to think about these things help to keep my mind sharp in such areas. There's a positive benefit to playing the game besides entertainment.
Now certainly, to each his own, regarding entertainment. To equate those two games though, is silly at best. It's like saying Chess and Candy Land are the same. Are they both games? Sure. Do they have comparable skill requirements or similar side-benefits bestowed to the player? Absolutely not. Does it make me an elitist for thinking that a game should have some challenge to overcome to be worth my time and mental capacity? Maybe.
Now if your wife pointed out that farmville and say...watching football were similar, I'd have to begrudgingly agree with her. I'll still insist that even watching a sporting event requires more thought than Farmville, but she'd be a lot closer than the comparison in the OP.