In this case, stay put, go public. Shadow organizations don't like the light.
If you run, you are separated from people who can support you. You lose access to your resources. If you run, you can be disappeared and no one will know, because you're on the run, right?
Since you're a witness - Let people know, tweet, do a blog about it. "Hey Joe, I saw the damnedest thing..." By doing this you have already accomplished the thing they wanted to prevent - your talking about it. Taking you out then is counterproductive. Taking you out would increase scrutiny of whatever you saw.
At this point you can sit back and wonder if they were really out to get you, or were you just paranoid. Hopefully you'll never know.