In the first Matrix movie, when Neo is arrested, Agent Smith tells him they just want help bringing a wanted terrorist to justice. That would be the infamous Morpheus. At the beginning of the movie, we see Trinity kill several police officers who have apprehended her. Later in the movie, Trinity & Neo storm a military building, killing security guards & soldiers while also detonating a bomb.

The thing is that all of these are envatted people. Morpheus at one explains to Neo that if someone is plugged in, then they're the enemy, because they will fight to protect the system (unless they want out), and agents can use their connection to jump into the digital representation of that person. Morpheus and his crew also inform Neo that if you die inside the Matrix, your mind makes it real, and you die for real.

As such, Neo kills human beings plugged into the Matrix without compunction to further the cause. How is this different from any terrorist or revolutionary group doing the same in the name of freedom? Granted, no civilians are ever shown being killed, and security forces are only killed if they get in the way. So it's not random terrorizing, nor is it done to terrorize. But it is still killing human beings who believe they are just doing their job.