If these trunks that you are talking about are members of the Port-Channel, then you just need to remove the VLAN from the Port-Channel and all the members will be updated using the command you said
switchport trunk allowed vlan rem 1411
As you are using rapid PVST, there is no need to remove the spanning instance as this will happen when you clear the VLAN from the switch configuration. In fact, if no ports/trunks are assigned and up in a VLAN, there will be no spanning-tree instance running.
You can verify this by doing :-
6509#show spanning-tree vlan x
and you will get the following :-
Spanning tree instance(s) for vlan x does not exist.