Yeah, I never used it in co-op. Heck, I never bothered with co-op except for a mission or two, of which I turned it off in those instances. And luckily, since the hack would sometimes make me get one shot, I never rose too high in Alliance Battle, coupled with the fact that the Alliance I am in seems to barely do it, I never looked suspicious. I am sure your characters also would be a red flag (which should go without saying). I stick to my maxed out Sharon Rogers, or Ancient One, and carry lower leveled characters along for EXP. Those characters are already good at soloing content, so high scores don't tend to come off as suspicious. All in all, just trying to say the hack is fun, and speeds things up a great deal, but you really have to stop yourself from abusing it, or the hammer will come down on you eventually.
Made the mistake of using it once in a real time battle(didn't realize that's what it was), I was soooo nervous haha. Sorry to hear what happened to you guys, though.