Yes, the access points would need a native VLAN on the trunk port. The native VLAN would just need to be different between the clusters.
For example:
VLAN10 = cliuster 1
VLAN 20 = cluster 2
All the ports connected to an AP in cluster 1 should have VLAN 10 as the native VLAN, and have all the user VLANs trunked. All the ports connected to an AP in cluster 2 should have VLAN 20 as the native VLAN, and have all of the user VLANs trunked.
The only difference between the ports on the clusters, should be the native (management VLAN for the cluster).