Tom makes a number of appearances throughout the usual storyline and the DLC expansions. The DLC missions are irrelevant to the main story and can be done after the main story, or at any time in parallel to the main story.
I'm not sure what you mean by being bothered by him. If you're referring to him inviting Rico to the starting point of a DLC mission, then you can simply keep ignoring that until you feel ready to do the mission.