We're overthinking again...
The Prime Directive exists in the TOS and TNG eras, and as long as it does, interfering with the Sioux aliens is a violation of it because they exist outside of Federation space. No special treaty is required to keep Starfleet from helping. All Starfleet and the Federation have to do is obey their own law.
In fact, in this situation their likely course of action would be to forcibly remove the settlers to Federation space, ending the prospecting and the story. They won't battle the aliens to protect the settlements.
This scenario can play out in any era the Prime Directive is in force. It doesn't have to be TOS.