I do not know whether the decision to use OWL Lite as the format for the ontology in S-RAMP was purely for modeling purposes or if the spec committee also intended for the other features of OWL Lite to be implemented. I suspect it was the former and not the latter.
Regardless, the disjointWith feature is not part of the OWL Lite spec and so would be out of scope for the S-RAMP spec as well.
That said, the S-RAMP spec is silent on a great many ontology related matters, including management of them within the repository. Currently the UI relies on Overlord specific APIs to manage the ontologies, including simply getting the list of ontologies installed in the repository. It uses Overlord specific APIs because the S-RAMP spec leaves ontology management up to the implementation (a mistake I believe, but a decision that predated my presence on the TC). Thus, I think it's reasonable to implement whatever ontology features we want within the UI.
Anything we might do in the repository implementation would need more careful consideration, so as not to violate the specification.