Short answer - no!
Why should their club be punished for the abhorrent behaviour of some of their fans at a neutral venue?
Steve Morison said on the pitch right after the game that they had "ruined" the moment - he was dead right, and it wasn't the club's fault.
Had it happened at the New Den in the semis of course, you might have a case.
BTW, I don't like Millwall, never have, so if you get your wish (I assume that's your wish?), I wouldn't shed a tear!