Pretty simple, once you have made the "innocent" civilian comply with your orders to get on his knees, beat the everloving ♥♥♥♥ out of him using your melee (press B for melee while holding a gun).

Its an old but effective way to do it, but it does the trick pretty well.

In this method, you need to have atleast one flashbang or stinger* equipped.
Then you simply throw it at them and they will not be very entertained by it.

In this method you need to have a taser equipped.
The method is executed by tasing someone even when they are complying (its better to do it multiple times so those "innocent" mofos can be taught a lesson).
If you dont have a taser, you can do it the Minnesota way, and just shoot them once in the chest with your sidearm.

Just shoot them, like straight up, just shoot em.

After those pesky bastards have "surrendered," just spam the "yell for compliance" key.

Now this method wont physically hurt them, but it will give them unforgettable trauma and maybe even PTSD.

When you have multiple "innocent civilians" all in a room, choose one you want to get traumatized, and just fan across the room with full auto on while making sure not to hit your teammates, or your target.