Among other things, reverse thrust and aerodynamic braking from spoilers aren't considered when calculating landing distance. Wheel brakes are.
An autobrake system modulates brakes for a set rate of acceleration (or deceleration, if you will). If reverse thrust is used, the same rate of acceleration will occur, but with less involvement of the brakes. You're out nothing by landing with autobrakes, and you still benefit from reverse with less brake energy when using reverse.
Autobrakes provide a known rate of acceleration, which means that it can be used to calculate stopping distance. In our own calculations, the Landin Data card spits cites the specific stopping distance with each level of braking applied; these distances don't change with or without reverse thrust, but the brake energy and subsequent brake temperature certainly does. If the calculation states that a medium autobrake setting will provide 6,000' of landing distance, then it provides it at the medium setting with or without the reverse thrust. With reverse thrust, the distance remains the same, but the brakes are cooler because the autobrake system uses the brakes less.
Autospoilers and ground spoiler systems are intended not to slow the aircraft, but to disrupt lift and put the weight on the wheels where the brakes can be more effective. This is their primary purpose, and consequently the brakes are the primary device for slowing the aircraft.
Additional braking which may be had from other features such as ground spoilers, reverse and anyother aerodynamic braking, are extra which may be applied to the ground acceleration (slowing) equation...but are not taken into account when calculating the distance...and shouldn't be relied upon given that they aren't permitted when calculating landing distance.
If your students are overusing the brake settings, then this is something to be included in the training. To instruct a student to not use, or disregard the autobrakes is to give away an efficient useful system for no good cause.
The autobrakes will always do a better and more consistent job of applying the brakes than you. Why would you not want to use them?
So far as "landing with the brakes applied," this doesn't happen with autobrakes. The delay applied to the braking system prevents landing with brakes applied, as does the antiskid bypass until the aircraft senses either truck tilt or weight on wheels...and as the autobrakes are part of the antiskid system, the concern of landing with a wheel locked up is eliminated by virtue of the fact that you're using the system to brake which prevents locked brakes.