I have a great solution. When someone fires so many swarmers, or builds a ship too big, or has too many docked entities that it starts breaking the server I open chat and say "oi, please cut that server breaking shit out. Thank you" :D
Works amazingly well surprisingly enough. The simplest solutions often do. 2000-3000 heat seekers bringing your server to a halt? Set a cap in the server rules maybe?
Rule 1.0 Do stupid and break the server and you'll be warned, kicked and possibly banned.
You're welcome.