How are you trying to delete the vlan interface?
I ask as the WebUI which I am guessing is being run AFTER running the set vsx off as VSX doesn't have the WebUI enabled is showing interfaces with IP from the VSX Network.
You won't be able to delete the bond1 until all of those sub-interfaces are removed.
I would expect that they are deleted in the SmartConsole for the VS that they are created in and then after the topology updates then says to install the security policy.
You said that did this but is contradicted by seeing the vlan interfaces exist in the WebUI which to access would need to have the VSX turned off.