It's difficult to set up that kind of large scale destruction facility safely in the middle of a war zone.
Add to that: There are people on the various sides who would be sorely tempted to shoot up the place and release the chemicals while wearing the uniforms etc of the other side.
The alternative is putting in a large and well armed security force (read that as some nation's troops) to stop the war.
The whole course of the past two years of UN and other negotiations have revolved around not being able to do that. At some points due to people not being willing to provide troops. At others because no agreement could be reached in the security council as to who the troops should shoot at.
So, packing them up and removing them from the country may well be the least bad option.