The IDSM-2 uses either Span or VACL Capture for monitoring.
In the case of Span as you said you could span the vlan that is being carried by the etherchannel.
Or you should also be able to Span the ports that are part of Etherchannel. (You don't span the EtherChannel, but rather the ports that are used in the EtherChannel). I checked the Cat 6K documentation for limitations on using EtherChannel ports as Span Source Ports and did not see any limitations or restrictions so it should be possible.
The other alternative is to use VACL Capture to monitor the packets on the vlans being carried by the EtherChannel. Since VACL is vlan based it doesn't matter whether or not the packets are from an etherchannel so you should not have any problem.