If you ask me, I think you are not scruffing your ferret hard enough.  A
ferret I had was rather ornery and prone to biting.  Taps on the nose and
flicking often did nothing more than give him a finger to bite.  The only
way I could control him was by scruffing and I mean really scruffing.  I
would grab him by his scruff, pick him up, and shake him (within reason).
If I scruffed him lightly, he would go nuts and try to bite, like yours.
 
I don't think you are hurting your fert, just annoying him.  Give him a good
scruff and shake.  My vet told me to do it that way.  She said it is
actually a quite natural way to handle them.  I have a little guy now who
must be the sweetest thing in the world.  I scruff him when his being
obnoxious.  It freezes him alright, but when I let go, there is no sign that
he was uncomfortable or hurt.  He just looks at me and then dooks around.
 
- Anthony
[Posted in FML issue 1546]