Dinesh, I thought something like that might have been the case (reason for 5.8.4).
So it sounds like you have a hierarchical topology also (VX9000 adopting site-controllers (RFS6000/7000 at some sites).
But to confirm: Yes, You can upgrade the controller separately from the APs. If the controller and APs are using different versions of WiNG, this just prevents you from being able to make configuration changes to the APs using the controller and then pushing those changes out from the controller. This is 100% intentional and is done to protect the operation of the APs. (*Sometimes* there are code differences between WiNG versions and there might be a case that if you pushed out a configuration change to an AP, the new config might contain a setting that the AP will not be compatible with the WiNG version on the AP)