So here's an idea I had recently that might just be a crazy theory, but I think would be interesting. Basically since the story of Whisper of the Worm is that we defeated Xol and then he went to Io and became a gun (sounds silly when you simplify it like that), I imagine that this gun isn't something we should just be using as much as we want with no consequences. It's undeniably one of the best weapons in the game being the ideal DPS weapon for many Guardians, but what if our abusing of the powerful weapon causes problems later? What if somehow us using the gun to kill so much ends up biting us in the a** later?
I don't know how they would do it without it just plain being annoying and frustrating to players, and I know people would miss their boss-melter, but what if we lose Whisper and somehow Xol uses the strength we've given him against us? What if when one of Oryx's sisters finally arrives, our favorite sniper rifle will turn against us?
I think it would be sucky to lose such a good gun, but a big twist with a change in the DPS meta could be a great move by Bungie if you ask me.