"Thrall" is not a listed game condition. "Flanking" is a listed game condition, the rules tell us exactly what it means. You need to not concentrate on figuring out what the word "thrall" means (I consider it to be simply flavor text) and look at the rest of the rules.
A master can do to his student exactly what it says he can do under "Rule of the Master" (plus since a master probably possesses a magical link to his student he can cast any magical link spell to make their lives miserable).
Likewise someone turned into a were-beast by the spell "Awful Rite of the Were-Beast" will do exactly what the spell says he will do: attempt to remain within 500 feet of the sorcerer and get a will save to break free every time the master gives a direct order. Expounding on this I note the line in the spell that says
the risk of losing control is just too great and few were-creatures created by this spell will hold back if they get a chance to attack their erstwhile master.
from that I deduce that a were-creature who is not
released from command is prevented from attacking the sorcerer, no direct order required. I would also rule that the order "protect me from anyone who attacks me" only ever needs to be given once, not each time the sorcerer is attacked. Fruthermore I notice the line in the spell that says
any time the sorcerer gives the target a direct order he must make a magic attack roll against the target's Will save to compel him to obey.
From that I conclude that the sorcorer is free to ask
the target to do something, using the normal rules for Diplomacy and Intimidate, without prompting a Will save. A sorcerer probably has many ways to charm/reward/punish his were-beast slave and so need only use the compulsion aspect of the spell when quick and sure results are required.
Hope that helps.