They probably figured out early they'd have to turn to that down the line, as the adult direwolves are way too big to be played by real dogs on set (without cumbersome trickery of the kind they used for hobbits in LOTR). They may have hoped to be able to use the CGI animal in concurrence with the real ones, according to the needs of each shots, which would have lowered costs).

For having been on maybe 20 shoots involving dogs, it's perfectly true they're a royal pain in the butt for the production (though it varies with breeds.. but those wolf-ish dogs they have on GoT aren't one of the "good breeds" for filming, as far as I know). They seriously limit what you can do in some scenes, ruins otherwise perfectly good takes, slow things down massively. It's really no wonder in scenes with animals, directors usually cut a lot between shots and try to keep the animal away from the shot with complex camera moves, or heavy in dialogue etc.