In the close shot of Jack O'Neill's boat starting, it is clearly still roped to the jetty. The very next shot shows the rope removed and the boat pulling away.
When the "Puddle Jumper" travels into the past, Teal'c states "the stars are different." Carter also notes "Earth was in a different orbit around the sun 5,000 years ago." Significant changes in the earth's orbit around the sun occur over millions not thousands of years. Even if the orbit had changed this would not affect the apparent positions of the stars. In fact, as seen from the Earth, the positions of the stars and constellations have changed very little in only 50 centuries.