Rights group Amnesty International said that during the clashes several people appeared to have been "summarily shot dead and their bodies dumped"
The Kenyan president has faced charges at the court over his alleged role in the deadly inter-ethnic violence after Kenya's 2007 elections.
The pilots' union has called for an indefinite strike in protest of "poor management". The airline says the threatened action has already cost it.
Alfred Olango fled a Ugandan region ravaged by conflict. His uncle in the town of Gulu expressed shock at killing.