At this point, the only way to resolve this is to punish the club. Not financially, that never does any good. Both West Ham and Millwall should be thrown out of the competition now and once an investigation has been conducted the club whose supporters are to blame should receive a severe points deduction.
I agree, throw the clubs out. I wouldn't be averse to some games without spectators for both clubs too.
People take their kids to see these clubs. It's despicable behaviour.