I couldn't imagine it being any more difficult than having to implement the AI allies that the game has currently. Hell, I definitely would have preferred having it be "just me and Friender against the world", rather than having to likely do more to babysit human allies that more than likely will just get in my way.
But hey, Mikami likes to have interesting surprises in his games (RE4 and God Hand both attest to that). Maybe the dog lives on in his OWN mode! 
It would be much more difficult. In current squad games, you do very little to order your teammates around. And another teammate is just another player walking about.
If you look at the dog correctly, he can be used as both cover and missile deployment. First of all, third person shooters like this are built on the tactical use of cover. Letting you place your own cover wherever you want would [tornado fang] up the game stage design severely. Second, having to control a second thingy along with your main character would be tricky, specially when doing stuff like cover fire for missiles. Do you place a marker with the second analog stick? Do you have to stand in one place while using it? Should the machine work similarly to the Mk II in MGS4?
It would be very complicated to implement something like this in a game. Maybe if they based part of the gameplay around it, it would work. But this is clearly a cool idea they had to throw around, and couldn't implement. I say save it for the sequel, and implement it PROPERLY. Make us proud.