Maybe if Sacagawea had been along the whole way, there would have been fewer confrontations. I’d go as far as to say probably. But it’s hard to say. There were a lot of friendly relations when Sacagawea was absent, and a couple of confrontations when Sacagawea was present.
The only shooting was with the Blackfoot along the Marias River in Montana. After agreeing to make camp together, the Indians tried to steal some horses in the middle of the night, and Lewis’s party attacked, killing two. The Indians returned fire, but missed. Sacagawea was absent.
The second-most serious confrontation was with the Lakota in South Dakota. They demanded a toll to proceed up the river. The Corps manned their guns, but there was no shooting. Sacagawea was absent.
South of the mouth of the Columbia, on the way back to Fort Clatsop from seeing the beached whale, an Indian tried to lure Pvt. McNeal away and kill him for his blanket. He escaped with help from other Indians. Sacagawea was in the same party as McNeal and was nearby.
Lewis punched an Indian for stealing near the Columbia River, following a series of minor thefts over several days. Sacagawea was present.
There were many friendly or mostly friendly meetings with Indians when Sacagawea was absent: with the Omaha, Osage, Missouri, Oto, Yankton Sioux, Arikara, Mandan, Hidatsa, and Shoshone. Sacagawea was present for part of the meetings with the last four tribes, but not for the initial meetings, which were all friendly.
Perhaps even more important in avoiding conflict than Sacagawea’s presence was the fact that the Corps, as long as it remained together, was a formidable fighting force. The expedition was much better armed than any of the Indians they met. Every man in the expedition had a good rifle, while the Indians mostly had a few old muskets among them. As far as the Great Falls of the Missouri, the Corps also had a small cannon. Other than the Blackfoots, there were a few other times when horses were stolen, but the Indians responsible were never seen. Importantly these incidents, like the skirmish with the Blackfoot and McNeal’s troubles, happened when the Corps was split up. As long as the Corps was together it would have been practically suicide to attack them, and none too smart to steal from them. Of the serious confrontations listed above, only the one with the Lakota happened when the Corps was all together, and the Lakota backed down as soon as the guns were manned.