But you're never going to be able to totally eliminate "clearance not available", so there will always be a need for pilots to action. Saying "no" must be a tool that's available to controllers. Trainees get flustered & bugger things up & do things a rated controller wouldn't do. That's just the nature of training. His denying a clearance was a minor contribution.
How hard is it to train pilots that if they're intending to request a clearance that they need a contingency plan in case they're knocked back? You have plan Bs for every phase of flight - abort the take-off, avoid that large patch of cloud, go around to avoid that cow. How hard is it to ask the trainee pilot to explain & implement what they'll do if denied a clearance?