the military may function as it's own separate entity, but the president is commander-in-chief of all the armed forces, so he's absolutely directly involved and completely responsible for the military's involvement in the fight to combat ebola in west Africa, having been the one to deploy the troops in the first place.
I don't understand at all your statement 'United States Goverment handles the Ebola crisis not only seperate from the military, but the state to state legislation differs. (working unilaterally)'
state to state legislation differs? unilaterally???
the president has insinuated himself into the manner in which individual states handle the ebola scare, specifically by making statements and taking a stand against what governors Cuomo and Christie felt was the proper way to handle the issue in their respective states. Obama has also taken it upon himself to appoint an 'ebola czar', increasing the federal government's role in the handling of the issue even further.
when you have a president ordering quarantines for the soldiers that he deploys, and at the same time speaking out against any such quarantines here at home, after having directly involved himself in how this is handled both in Africa and domestically, then you indeed have a hypocritical handling of things.