You have to think about the game as a whole. It's too time consuming to work in a k9. How does the dog get into a vehicle for one? As soon as your Ghost opens a car door, he or she immediately gets in. Does the dog crash through a passenger window to get in? Getting into a boat on the water will not be an easy task for the dog to do on its own. How does one sky dive with the canine, especially in the case your aircraft gets hit with a SAM? This is just issues with vehicles. Now imagine playing the story missions. How will the dog fare against fighting Walker? Or all of the drones in the final Splinter Cell crossover mission? Then there are really immersive "breakingpoints." Your Ghost climbs a ladder to get to a roof top, how does the dog magically appear next to you on the roof without wondering how the hell the dog found it's way up?
There are too many obstacles and player choices to take into consideration that having a k9 simply won't work out well.