When I met Preston, I was honestly pitying his desperate pleas for help. So, big deal, I helped him, and then a few settlements, and then MORE settlements, before having enough to take over The Castle.
This was all well and good, but subsequent playthroughs made me hate Preston for being lazy af (I'm your general, not your errand boi). So it is with horrible realization that I realized that I can't cleanup The Castle without being Preston's b****.
Wiki says you could use a console command to clean up mess, but that only applied to the mud heaps, not the egg debris - which, for some reason, are immune to everything ranging from grenades to nukes. Makes me wonder if there's a mod out there that makes walls out of Mirelurk stuff (The Mariner doesn't count). The workaround to this was to click each individual mirelurk egg 'corpse' then console command disable. And this has to be done every time you clear The Castle without the minutemen. As my number of playthroughs increased, so did my irritation of having to clear this magnificent holdout point.
TLDR, I hate Preston, minutemen are farmers with self-interest, Mirelurk eggs are nuke-proof, made console compilation to rid of these eggs.
Just put the batch file into where your Fallout.exe is located, head in game, open console and type "bat omelette".
Recommend you do this AFTER clearing the castle. The other mirelurks disappear overtime, but the queen's corpse for some reason does not decay. I did not include her in this and must be manually disabled by you, because I like having that corpse around. I like building flaming altars around that magnificent shell.