So if only 5 of your vlans have an interface on the cat6509, then this must mean the other vlans are restricted only to communicate WITHIN the vlan. In order for each vlan to have inline protection between them, you would have to create a dummy vlan for each production vlan and set up inline vlan pairs on the IDSM. (I am making an assumption here) Of course, the same would hold true on IDS appliance, given that you have enough interfaces (you create an inline interface pair).
Alternatively, you could set up SPAN or VACLs for all of the vlans you want protected. Of course, you are losing the IPS capabilities to an extent as this would be more of an IDS solution. You could add blocking devices to the sensor and set the action to block host for the signatures that you want to blocked against.
HTH