Yeah, the Suicide Squad isn't supposed to be a good thing. Its not portrayed as morally right, in fact in the comics whenever a hero learns about it they're generally horrified. Amanda Waller is so extreme in her actions that she's generally considered a villain herself. Heck, the heroes have had to take her down specifically several times when she crosses one too many lines. In current comics she's so drunk with power she's trying to go back on a deal with Batman and capture him (along with the reformed Killer Frost), and this is after she tried to take down the Justice League. Neither the SS or Waller are portrayed as good guys in the comics. They mostly fight bad guys, but that doesn't make them good guys (although Waller certainly thinks shes a good guy).