@mseaton is correct. Our vision for making these connections was through Episodes of Care. We planned for this in 2009, but there has not been demand for it until now. We could re-visit the design to update it and ensure it meets expectations (e.g., link to program), but the intent was that an “episode” would be a collection of 1-to-n visits and/or encounters that relate to a specific condition or treatment plan (program).
I think Episodes of Care could meet your need and add flexibility. For example, instead of creating a single link of an encounter to a program, an “episode” would allow an encounter to be linked to 0-to-n programs or conditions.
Cheers,
-Burke 
How this relates to FHIR
FHIR’s Encounter resource uses a simple hierarchy (Encounter.partOf) to allow a FHIR Encounter to represent our Visit, Encounter, or an Episode of Care.
Our design (distinguishing between Visit, Encounter, and Episode) makes the distinctions explicit and has the benefit of allowing an encounter to be part of a visit and/or part of 0-to-n episodes of care.