(For discussion only - only criticism of the controller implied or intended.)
Why not just leave the departure at the holding point, given that rwy configuration? The report states that traffic levels were not high, so no need to be super expeditious. Wait till the landing a/c has passed - which you have to do anyway obviously - then clear the departure for take-off from the holding point. Saves you one transmission and limits any risk of exactly what happened.
Further thought: it seems that there are two holding points adjacent to the landing rwy - from memory, C5 & C6. Seems that the latter might be way too close for comfort to the landing runway. Is there any possibility - and/or mitigations in place - that the pilots of departing a/c might inadvertently go to the wrong one? (Don't have the report open so that is from memory....) Anyone familiar with the procedures?