The 7th level in HeroLab is probably based on using it as a mount. These things presume you're using the critter in the most optimal way the author can think of, so think of the dire wolf as a tripping mount, wearing barding, negating hits with Mounted Combat. Is that worth 2 levels of adjustment? I personally don't think so, but that's likely where they're coming from.
It would not be two levels of adjustment because an awake dire wolf is 7 hit dice, not 5 like normal dire wolf. with effective bab as 7 level 3/4 bab class with 7 levels saves, feats, and ability points.
I think Awaken Animal fit in at what ever their hit dice is to be uses as cohorts, their stats are going to be higher then normal npc, especial after they get their 1st class level in actual class and get the ability boost from that. from the monster rules "Creatures with class levels receive +4, +4, +2, +2, +0, and –2 adjustments to their ability scores."