Add a module like "Missile Stage Separator" with parameters for stage separation. The last part of a missile will be ejected and deleted. If the missile projectile doesn't really work like that, it can transform mid-flight into a different, smaller missile depending on missile design.
Primary use is to add boost phases for niche missiles or separating short-range/variable thrusters from torpedo segment for anti-submarine missiles that no longer have 4x drag when hitting the water, but retain it in the initial flight until segment separation.