After this, the completion of the quest may cause everything there to get cleaned up. It's possible that something similar will occur with Preston. Deb paid me, and had some dialog that was scripted for that very occasion. I selected that, and the quest started and finished right away.
One of my dialog choices was 'I've already taken care of those ghouls'. By the time I first got to Bunker Hill, I had probably already cleared these ghouls out like a dozen times. Deb in Bunker Hill asks you to clear out the ghouls at the National Guard Training Yard. If you join the Minutemen, it's possible that when Preston first mentions taking the Castle back, that you'll get a dialog option like 'I've already done that.' This has happened to me with a few other (admittedly much more minor) quests. I highly recommend following the discussions at AFK mods, as any new developments or changes to the cleaning procedure will appear there first. It's been a while, but I seem to recall Preston even saying something along the lines of 'we'll start cleaning this mess up while you get the radio up and running.' Shortly thereafter, the queen, the eggs, and all of the other random mirelurks were cleaned up. AFK Mods is planning an official cleaning guide, but has held off publishing it pending the final creation kit updates. As the others have said, since cleaning all of this stuff up is directly related to a quest, I doubt that it'll clean itself up without actually completing the quest.
