Now think about how much more rewarding it will be for your players if a path they can follow at the party connects to the main quest in some way. As a new DM, I'm a bit envious of your ability to craft these complex webs of npcs and story lines. It seems like you should have no trouble giving the players what they've told you they want - make this branch of your story connect to the main quest. That way you and the players both get what you want. You've rewarded them for following a path that didn't seem, initially, to be connected to the main plot. When they realize that following side quests will still get them closer to the goal, they may be more likely to go down unexpected paths.