Although there are ways to avoid it as people have been very quick to point out. The OP is right, you shouldn't have to avoid this poor game mechanic in the first place. If I saw a police officer chasing a shop lifter and I stepped in to help.... and in the process bumped into the officer I was helping I would be a bit surprised if I was given the electric chair. Certainly what is needed is a few permitted hits and warning messages as with most other space combat games in the past.
Yes but its not bumping is it, hitting means hitting with gunfire, if you tried to help the police and ended up shooting one in the shoulder by accident I think you would face prosecution, though probably not the electric chair. The thing is the OP did not understand how to slip past the station scans using silent running nor even the need to do so. Now they do and hopefully others can learn from their experience. I honestly think that these game rules do make sense and are worth having as they make the game more fun by introducing genuine risks with effective means to survive them in game.
What would help is a fairly explicit explanation of these mechanics in the manual and in particular the tute missions should provide a practice mission for docking unscanned with a warrant outstanding.