<<would I be correct to say the civilian craft has right of way considering that a supersonic aircraft is typically smaller and more manouverable (agile) than a commercial airliner. >>
I don't know about the country where the incident happened but the UK Rules of the Air make no distinction between different types of powered flying machine. There are various rules which should have prevented the incident but ATC should have sorted the problem too. Here are a couple of excerpts from the UK Rules (note "flying machines" does not mention type):
(a) flying machines shall give way to airships, gliders and balloons;
(b) airships shall give way to gliders and balloons;
(c) gliders shall give way to balloons.
(2) Mechanically driven aircraft shall give way to aircraft which are towing other aircraft or objects.
and
11.—(1) Subject to paragraph (3), an aircraft which is being overtaken in the air shall have the right-of-way and the overtaking aircraft, whether climbing, descending or in horizontal flight, shall keep out of the way of the other aircraft by altering course to the right.