So the problem is that in movies they try to make things personal? Because it happens in every movie. At the end the bad guy will always take a relative hostage. In Die Hard everything is personal, in the first two movies John McClane has to rescue his wife, in the third one the main villain just happens to be the brother of the first movie's villain and in the fourth one his daughter is kidnapped.
How many times the partner of the cop/fbi/cia/secret service agent is the bad guy? Or his superior. How many times the cop has to drop the case because he's too involved?
Even in the holy Batman trilogy by Christopher Nolan things become personal because Rachel is the target of the bad guys in the first two movies (in the second she just happens to be the girlfriend of Harvey Dent) and in the third:
Especially in comics these things happen, mortal enemies that are friends (Xavier - Magneto), brothers (Thor - Loki), clones (Cable - Stryfe), acquaintances (Peter Parker - Norman Osborn). Since comic book movies are based on comics these relationships are usually present in the movies as well.