We are also runners that have hiked to petite cayes twice. First time we parked near the dump across from Pinel island and hiked about 35-40 minutes. The hike is over a lot of broken conch shells. Some of the hike has a path. The downside of hiking from this side is the car did not feel very secure. You just park along the beach in no mans land.
The second time we drove into the Anse Marcel area and parked. Car felt way more secure. Big populated parking lots. You have to find the start of the path. Park to the first open lot on your right after driving down the hill into Anse Marcel. Now you have to start hiking down a service road on the opposite side of the marina. When you see a green water tank you walk in behind it and pick up the path. It is a steep and rocky path with a lot of stove pipe cactus along the way. About a 45 minute hike. View the path from google maps satellite view.
It is kind of a coin toss which is better, but we did not worry about the car from the Anse Marcel side.