There is currently no way to prevent this situation. It sounds like in theory a process advisor/precondition could be created for the deliver operation, which would make sure that the user delivers all change sets associated to a particular work item - all at the same time, otherwise it would fail... however in practice I can't see that many teams would want to enforce such a check.

This sounds more like a generic issue though in that there could be a case where an author has two change sets, and the code review was conducted which also had no issues (or even no code review was conducted), and the author could accidentally deliver only one of the two change sets, which in the end results in 'incomplete' code delivered to the stream.

Note: If this situation is of some concern, then this could be made into a manual process by also 'informally' requiring a approval or verification on the work item to ensure that all changes have been delivered. Fortunately, the actual checking of this would be pretty straightforward using the Locate Change Sets editor.