It is very hard to get two planes at the same place at the same time even if you are trying to do so. It is only when they are on the ground or in the process of takeoff or landing where - if everything is done wrong - they possibly could bump into each other.
An aircraft like this would present no hazard to commercial aviation. Just like any aircraft in controlled flight, it would follow a specific path to its target altitude. This one would stay three times higher than any civil traffic doing circles for a long time. It would then descend along another closely controlled flight path when its mission is over. Just because it is unmanned doesn't mean it is just flying around willy-nilly. It is still closely controlled both from the ground and internally. All aircraft in controlled airspace (manned or unmanned) will follow the same flight rules, and these have very wide margins of safety built in.