You cannot filter data based upon the qualities of items in collections it contains. For example you could not return Stories with no children or defects. You could filter change the query to return the children of the stories if you wanted. This would enable you to filter the stories in memory on the browser side.
There are a few issues with this plan that kept me from filtering them when we wrote the Kanban App. If the the first page of stories returned contained entirely epics for one of the columns queries you would end up with a column with no data in it even if further down rank you had leaf stories that you would of been shown.
The second issue is that due to the Rally's WSAPI ability to fetch fields semi-recursively each child object can be rather large. Some of our customers have a single epic with many many children I didn't want to chance the lack of responsiveness for those customers.
If you are comfortable with this issues on your personal version of our Kanban board you can just listen to the onDataRetrieved event and filter out your unwanted stories.
Internally we are very aware of the annoyances that this causes and we are working to find a good general solution to this issue.
If we release one I will dig this post back up and make sure the new solution is explained.