Okay, now that it isn't 15 minutes before my game and I have had a chance to sleep, I have a few more thoughts.
The first is that riding a flying animal requires an exotic saddle. This costs 60 gold and would generally be beyond the means of a ranger starting out (barring using starting gold instead of gear and having a lucky roll). The griffon and wyvern saddles found after the battle would not fit the giant eagle.
The second is that (at least in my games) large beasts are not allowed inside cities. This would include Gate Pass, Bresk, and Seaquen (at least at first, before they save the city). So the giant eagle would be hanging out outside the city during the first adventure. It would have to stay away during the midnight battle, and the city defenses would keep it out during the next day. The heroes would then be able to hook up with the giant eagle outside of the city, and it could signal that there is danger ahead during the gauntlet or that enemies are approaching at the farmhouse. Honestly, an extra fighter there would be helpful, and it would mean that Crystin and Haddin could likely stay out of the fight (in my game, Haddin mind controlled Smiley for a bit).
The third thought is that it would be interesting for the giant eagle to be infected with the indomitable fire in the second adventure. If this happens after they talk to Indomitability and Kazyk, their suggestions of letting the creatures on fire die with the forest will seem less sinister. After the giant eagle becomes infected, the heroes would likely rethink any agreement with those entities.
Once the heroes reach Seaquen, the ranger can get an exotic saddle made, and having a flying mount will be useful but not game breaking. If the giant eagle is doing too much damage, you can always add a difficulty level to some (but probably not all) of the encounters where the eagle will be present.