I wasn't fully aware about these "flag wars" but you put it very well; everyone should have a freedom to express their opinions as long as it isn't hate speech, trolling ect. no matter how ridiculous they might seem.
Flagging should be left for what it's for: to eliminate spam and plagiarism, not to be used as childishly expressing hate or disagreement on people for their opinions by ruining their rewards.
It's not even the rewards in many cases, some get flagged to a rep of 0 or even negative values. It's possible to recover from a $0.00 payout, but try coming back from a -1 reputation without the help of friends!
Ah, I didn't even realize the reputation being hurt! That makes it even worse for them who get targeted by unreasonable hate.