The devs need to change pips to scale off of account rank and whether or not the match was a win or a loss (not season ranking, but your rank #) like WvW, but then when they punish people for botting or manipulation, nuke their rank. And also do a better job of detecting that. Doing this will make smurf accounts worthless (because nowadays you can use your free pips to earn gold from losses and send it to a main account), and also nuke the main accounts' progress/ability to earn legendary rewards and currency. Right now, bad behavior is too incentivized and given Anet is gunshy about permabans, there's really no consequences, so no active discouragement from trying again. That's the issue (I would say in addition to allowing FTP accounts to play ranked, that just makes it too easy to throw bots and smurf accounts into the mix). If your rewards scale off of both your dedication to the game mode and your win rate, I believe that's the best model and if that progress can be reset when cheating occurs, it will actively discourage it.
Though I think the game mode as a whole needs more to it than just conquest if it's going to survive long term after the new influx of players. If anet fails to fix matchmaking and manipulation before this game goes to steam, it's a lost opportunity to save the game mode. I also think they need to introduce a separate queue for complete premades. And maybe kill duo altogether. It's just solo and/or premades against each other (but never mixed. Premades are never matched against solo players).