I agree, the missile system for heat seeking should be given some safety features but I must admit this is one of the best weapons I have equip on my super structures. Not a system that should be used around allies or ships, bases, esc. Great for fending off small irritating ships when massive cruise has a turn ratio of 0.0.0.0, when using this weapon I make sure that all crew find there way into a none essential or independent system block, which actually protects them from being killed by the missiles. It just boils down to using the missile system responsibly. When I pull up to an enemy station or pirate infestation I make sure that I am far enough from the fleet and that crew are in safe blocks then I go to town and lay waist to all enemy. Its very effective weapon, and I support its use if used correctly. I like to build and repurpose super cruisers, and I have finished a Variant of the Super Star Destroyer, and now it looks like its on steroids and is not to be trifold with. If I were to go into deep space with it I would feel safe from just about anything out there. :D Anyways so keep that in mind if you have crew on your ship have non essential blocks or independent weapon system blocks that they can get into and keep a distance from the rest of your fleet if accompanied, use communication to alleviate fleet issues, that will solve most of your issues with the heat seekers.
Cheers :D