Following someone as they run away can be used in your documentary, but you need to prepare well and know what your purpose is.
Controversial topics are what the clandestine freedom of the guerilla filmmaker was born for. Film, as a form of journalism, has the responsibility to act as a form of independent checks and balances of the dominant governmental and private institutions. Confrontation like this often comes face to face when you want to ask an acting individual serious questions or expose their behavior. Running from the camera is a common response, but continuing to get them on film may be the kind of footage that you need to display their refusal to engage you reasonably. When chasing someone you have to take special considerations both for your footage and for your equipment.
A video following someone will never be successful unless this was planned for ahead of time. Of course you never know for sure when someone might flee, but if you have any indication that there is a possibility of it you need to keep that in mind during your production preparation. Keep in mind that you may be running with the camera, and that you may need to protect yourself. If you can get a steadicam, this would be the time to do this.
The Buffer Interviewer
Keep someone separate from the camera asking questions or at least diverting attention. This will come in handy when trying to get answers, which the confrontation may inspire. Also it will act as a deflection shield in case the subject attempts to attack you. This person can defend the camera person, who should be trying to get that aggressive footage. Keep in mind that a person does not have the right to touch your camera in a public area and if they respond to you like that then you have the right to defend yourself as if you were being attacked with violent force.
Keep the other person micro-phoned with a wireless microphone at all times, though you may also want to give them a hand microphone to ask questions. Also run the onboard microphone on your camera so you are getting several channels of sound at different locations in the situation.
Keep it Small
Keep the camera you are using both small and stable. Do not try to use an excessively heavy shoulder mounted camera because it will weigh you down and can hurt you. Try to use a lightweight digital camera that also retains a pretty stable image as it is being bounced around.
It Is What It Is
Do not try and make the video look as though you are not chasing them. Use the situation for what it is and do not try and use it as some standard B-roll. It is a video of them being followed so make sure that is the kind of footage you intend to take.
Try running ahead of the person, then stopping and following them while you remain stationary. No matter what, you are trying to show them escaping, not just getting normal footage of them. This is fine in a public area, but if you get on private property you could be subject to trespassing laws. The purpose of this is to raise the stakes and to put pressure on the individual, so make sure that this is what you want to do.