Stopping all trains is certainly safer than them colliding. But, unless it is for a very short period, it is not safe unless all the (passenger) trains are stopped at an appropriate platform where passengers can disembark. If trains are stopped elsewhere, then risks arise from passengers being trapped onboard or, worse, passengers may 'self-evacuate' into a potentially very hazardous environment with moving trains (yes, all trains have stopped but they will start moving again at some point), in some places lethal voltages from third rails, etc. Trains being stopped by loss of signalling and comms isn't as bad as being stopped by loss of power (resulting in loss of onboard HVAC), but still, it ain't safe.
