You're taking it out of context. The Harkonnens were sent to take over shop on Arrakkis. That specific space for the on land was partially occupied by that group of Fremen. That group didn't like what was happening, so they declared war on the Harkonnens. It was more of an annoyance than anything. They're outgunned, but have the advantage of the desert but that specific group is at war, but I forget who took the first shot, but there are no Fremen slaves. The Harkonnens even know where the rest of that group lived, they just don't care. The resources on their planet is being exploited, and if either see the other, it's on-site. The Harkonnens didn't even live there. Overall, the Fremen are free to do what they want to do..which is why the other tribes don't even matter in the grand scheme of things.
If Leto came in with the target practice savagery, that group would've declared war on him. He didn't bother them, so they weren't gonna bother him. That's partially what the meeting with Stilgar was about. But he sent down Duncan as an ambassador and scout, so that he could recruit them as allies. He knew his appointment was a trap. If this was a white savior story, Leto is technically the one, since he unseated the Harkonnens.