Is there anyway I can set their hostility or aggression levels, I'm spawning stormcloaks afterall so a little surprised they're not attacking the Thalmor on sight anyway!
If you can use the console (PC only), then yes, it looks possible. There are two Actor Values that may do what you want:
Aggression (0-3) unagressive, aggressive, very aggressive, frenzied
Confidence (0-4) cowardly, cautious, average, brave, foolhardy
You would open the console, target your chicken and enter "setav aggression 2" for very or maybe 3 for frenzy
and then "setav confidence 3" for brave, or maybe 4 for foolhardy
Just for your information, if you first use "getav aggression", and "getav confidence" you can maybe find out if your chicken is designed that way (if you get 0's as a result). If not, maybe they are being hit by a fear effect.
Getavinfo instead of just getav gives you the same info, but with maybe a little more detail.
Good luck.