Yes, you can do this using event action rules/filters. Create a filter, which would exclude “deny†or “block†action from the VA scanner IP to any IP (or a subnet), which is applicable for signatures 900-65355 (default) . It is pretty easy to do once you are in the event action filter screen.
Assuming that you still want to fire events for the scanner events, but want to avoid blocking it. Incase you wouldn't need alerts either, have those actions too selected to have subtracted from a fired event.
http://www.cisco.com/en/US/docs/security/ips/6.2/configuration/guide/cli/cli_event_action_rules.html
