The answer would be for the aircraft not to have been cleared for the SID in the first place.
if thats the case, there are gonna be a hell of a lot of delays in the TMA, as we constantly have a/c on cat B flights operating below sid altitudes, often for several hours on end.
The clearance was safe and the SID should have been issued, with the level amendment, as per
turn it offs post.
what is not known, is how it was phrased. Yes, it is a step climb, so the pilot should be left in absolutely no doubt that he has to stop totally at a given altitude and the reason ahould be given, to amplify.
I don't work in a tower but something along the lines of "C/S maintain 4000' on departure there will be traffic above" wait for acknowledgement, then "C/S cleared for take off....."