OP is pretending to be reasonable, but is really insisting that there should be *no* repercussions for hitting a security ship with a missile, because it's an "accident". There's already a pretty decent system in place to handle this, and if you really think it through its more than fair. If you are in a live-fire situation and you have an "oopsie" with your missile launcher, you are slapped with a *small* bounty which only lasts for a short amount of time before turning into a minor fine. The effect here is that the bounty is your cue to Get The F Out of there because as far as the authorities are concerned you are not welcome, and are more of a liability than an asset.
The fiction of Elite is essentially a libertarian dystopia scenario where every profession has been largely reduced to being an Uber driver, and even entire *wars* are outsourced. Imagine if there were an UBER for law enforcement- that's basically the Pilot's Federation. Now imagine that the NYPD is severely understaffed and underfunded, and they are forced to work alongside any random yahoo who shows up at the scene of a crime to "help" - that's basically us.
Imagine that an UBER-cop drives his hot pink camero to the scene of a crime, squealing his tires as he comes to a stop in the bus lane, side swiping a park bench in the process, while the NYPD are midway through apprehending a wanted criminal. He hops out of his car, climbs onto the hood, and yells "I got this!" as he pulls out a pair of gold-plated Glock-19 pistols from twin shoulder holsters, before opening fire in the general direction of the criminal, over the heads of the cops. Stray bullets shatter the rear windshield of one of the cop cars, and another officer has his hat shot off.
"Oops, sorry!" He shouts, "no harm no foul, right?" barely audible over the staccato of his pistols, which he is *still firing*.
Now imagine that this kind of thing happens *all the time*. Now imagine that in addition to incompetent and overzealous Amateurs periodically showing up, you also occasionally have to contend with dedicated assassins who show up *specifically to kill cops*. And the assassins are also "crowdsourced" and paid by the same company as the rent-a-cops.
Being violently chased from the scene of the crime and given a 15 minute "time out" is more than fair.