Remove the water from the zucchini pasta by placing it on a paper towel. Generously sprinkle sea salt over all of the zoodles and let sit for 20 minutes. This will pull the moisture out of the zoodles so they are not soggy.
While the zoodles sit, make the pesto. In a food processor, puree the basil, pine nuts, garlic, olive oil, salt, and pepper for 2 minutes, or until fully smooth. Using another paper towel, pat the zoodles dry.
In a medium saucepan over medium heat, warm the coconut oil. Add the zoodles to the pan with ½ cup of pesto and diced tomato. Cook, stirring occasionally,for 5 minutes, or until the zoodles are warm.
Garnish with any leftover pine nuts and preserve the remaining pesto for later use.