I honestly think it's mainly there to make people think about what they're doing, as Ed has said. If you go into Security and you have no idea Intent means different things for certain situations, you kinda deserve a tazer to the face.
I could go in depth if you want, but I feel I may be over analyzing the shit out of this.
As security, your job is to try to bring in crimers whenever possible (to make it more challenging for bad guys). Your baton is set to be ready to do this, right out the box locker, and the only other weapons you have without HoS clearance are the tazer, the flash, and flashbangs. The baton is pretty much the only thing that can do lethal harm reliably, so after stunning someone safely, you have to switch it so you're killing someone rather than safely trying to bring them in (I suppose as literal turning the safety off as you can get). Turning safety off takes a bit of time, meaning you have a small amount of time to determine if it's really necessary (usually the answer is OF FUCKING COURSE IT IS, but go with it for a moment). Basically, not removing the safety and attacking someone with it is the game reminding you to consider your actions and punishing you for it (hopefully with repeated farting on and looting of you at worst)