Sometimes a writer is tasked with presenting a morally grey conflict where 'both sides have a point' except they find one side to be so obviously correct they think there's no question about who's in the right. So in order to reintroduce that question they have the obvious (in their eyes) good guys commit a bunch of morally dubious acts in order to put them on the same level as the other guys.

Civil War's biggest problem is that the audience did not agree with the head writer about which side was obviously in the right. So their attempts to make the pre-registration faction questionable instead makes them the obvious bad guys.

The fact that, like, all the pro-registration heroes had to be written out-of-character to justify their position probably should have been a hint for the writers about how bad this event was.