I agree, some change must be made, a lot of times the people committing these mistakes and breaking the rules are new users, maybe instead of flagging on the first time, a strike system could be used, instead of nuking the account to -1 rep for the first bad post and provide a rehabilitation system? maybe when delivering the warnings also leaving them a link to the site rules and the community consensus on plagiarism and copy/pasting instead of flagging them and not telling them why?

Flags don't need to go away, they just need to be used properly.