The extraterrestrial diseases would likely be of little threat. Yes, terrestrial and extraterrestrial life have never encountered each other...and that is exactly why they would likely have no effect! It requires complementary cellular biology. Earth diseases and earth life have evolved with each other for millions of years. They have the chemical compatibility to interact and interface with each other. An alien disease would lack this compatibility - they could not infect earth life, and earth life could not infect them. Take, for instance, a space virus. Viruses use surface proteins to bind to cell receptors and begin their infection. if the cell is expecting one protein, and the virus can only produce a protein not found on earth, then absolutely nothing would happen. The space virus couldn't infect because it doesn't recognize the cell as infectable, and the white blood cells couldn't identify the virus as a threat. Similarly, if a human went to a new planet and tried to eat the flora and fauna, they would likely not be able to digest it. if an alien came to earth, they could not eat earth flora and fauna. There's no compatibility.
Now, handwaving this is fine, such as by a creator xenos that used a standard template across multiple planets, xenos engineered for their environment, or "because author said so" but in reality there is little to worry about without common molecular code.