I'm not 100%, but we always played it if the unit was destroyed (such as all the rank and file being killed in close combat but the characters survived) then the opponent would get the Vps For the unit but not any characters that were alive. If the unit fled and was destroyed via being run down then the characters would also be slain and they'd get Vps for the unit AND the characters as they'd all be removed.
Our justification of this is your characters can (generally) leave a unit during your turn so they aren't really a part of the unit when it comes down to rewarding VPs.
So if my 300pt tyrant in my 300 Bull unit was in combat and they killed all my bulls (ouch!) but NOT my tyrant it would give them 300pts only, but if they ran them down they'd get all 600, if that makes sense

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However, I admittedly don't have any rule book pages to verify it, that's just how we play it and I thought was how it was supposed to be!