Actually, the eggs aren't untouchable! Just build over to a pile of eggs, put a tentacle over them, and they'll slowly be destroyed.
Also, my general go-to strategy has been to clear out underground cavities to put important organs in. If anything manages to get past my defenses, I just destroy the sensitive stuff, build tentacles, and let them destroy whatever is being problematic. You should have decent upgrades by the time you're big enough to have such a problem, at least. :P
But if the space with an egg is already occupied by a body section or organ, there are times when a connection simply can't be temporarily sacrificed. For example, I've had several unlucky maps where chunks of ruins created bottlenecks where large sections of creature had to be connected by narrow tendrils of body sections with no room for defenses.
Eggs also seem to spontaneously respawn in closed cavities and occupied tiles- there are numerous times where I've come back to closed cavities surrounded by defenses to find a new batch of centipedes chewing up organs, despite having very definitely cleared the cavity out before.
Eggs being invulnerable to passive contact damage but having to be laid by an existing enemy (meaning you can clear and defend an area but breached defenses are very dangerous) could be fun.
Eggs being able to respawn anywhere but being vulnerable to contact damage could be fun. (You could passively block eggs by filling an area with creature)
Contact-damage-proof eggs spawning anywhere but also having an organ that blocks or damages them in a certain radius could also be fun (strategy about where to place the defense organs and how many you need, potential for upgrades turning eggs to resources, etc.)
Eggs ignoring your internal defenses and randomly destroying sections of your creature with no way to prevent this other than destroying those sections first? Not fun.