You have to understand your enemy, and develop a battle plan.
Mine is based on education,diversion and using the darkness.
Education: My wife has learned the importance of Civilization to me. She knows that she and Civ are on equal ground, and must learn to live in unison with each other.
Diversion: Civ is a great way to pass the time. Not everyone has the luxury of having a hobby that can keep you occupied for days on end, with the ability to stop and resume whenever you like. I try to find ways to keep my wife occupied - books, movies, hobbies etc so she doesn't feel like bothering me in the middle of a campaign.
Darkness - what better time to play Civ than at night, after loved ones have gone to bed. There is the risk you won't actually make it to bed, so an alternative is to get up super early and squeeze in a few turns before work.
And the laptop idea someone mentioned above is super. Take the laptop in front of TV, in bed while spouse is reading, or even on holiday while everyone else gets sunburned at the beach. A great way to mix "family time" with "civ time".