That's kind of what I expected\was afraid of.
Is such a functionality on the roadmap at all? I have to think this is a pretty big gap for a lot of organizations our size. In theory I could get around it by running the patch scan from console and then scheduling deployment, but that defeats the purpose that directed us toward going with an agent-based configuration in the first place.
It's something we are looking at and I agree a optional feature like that would be a good addition. I know the PM would like to see a feature request for this.
Done, hope to see something like this added!