Letting the driver off whenever the team breaks a rule would have pretty disastrous consequences. There'd be an incentive to unsafely release, there'd be an incentive to run out-of-spec components, there'd be an incentive to mess with tyre pressures, there'd be an incentive to mess with the fuel load, etc.

I agree with your take in general (though the out-of-specs part usage seems a little too far-fetched). What my point is that it is a minor infraction with little to no bearing on the qualifying session and very little actual risk (as they weren't fighting for position so there is no scramble to minimise time in the pit lane). Giving a grid penalty taking into account the above points would have been unbelievably harsh