My opinion is that they did not want to shoot her until she started running away again. For whatever reason. I do not debate that they had the manpower, the gunpower, the upper hand, whatever else you want to throw in there, because exactly as you say - if they had wanted to, they would have.....
With the assistance of God??....not for me to judge. She certainly survived by the hair of her chinny-chin-chin. If she felt God was with her, who am I to argue that?
This is semantics. I do not believe they "let" her go. I believe she escaped. I feel that until she ran after trying to get David, she had value to them (ransom, trafficking, plaything ??? Your guess is as good as mine.) Once she ran the second time, it became stop her, above all else, which is why they followed her back to the US IMO for the very reason you discuss. She, and her story are bad for business. I really think this happened very quickly and they did not know what to do. I don't think they really planned on killing David, but it happened and then it became "what do we do now?". That is why I think they went back to confer with the other boats when she decided to run. And at that point bullet holes would be a good thing - they wanted her dead once she started running again. She said she was on the side of the jet ski, putting it between her and them, until she got enough distance to feel safe.
You are correct though. If they watched her run aground, they should know who was there. I thought I had read that he owned a home there, but something else said he took the day off work....IDK. If he was just John Q. Civilian I would think he would be hard to ID without seeing his face.
But to answer your question directly - I don't think they "allowed" her to do anything. Tiffany escaped. Horse of a different color.