I think it's a good idea delete the fly command, I have to reasons why that will be a correct idea
1) The idea of the AC server is to make parkours and have fun crossing all the map. Having fly changes the idea of making parkours to farming gold. Sponsors players with fly will have a lot of gold bacause of the fly command, with the gold you can buy better armors and weapons, therefore, those players will unbalance the PVP situations in the moddality. If the fly is deleted, the amount of gold that enter in the economy of the server will decrease a lot (making the market active again, in the case of a wipe in AC) reducing the amount of players with OP weapons. It's not necessary the idea of checkpoints, because the premium/sponsor players have the tpa command, it's not the same but it's enought.
2) The amount of reports about fly pvp abuse and lag because fly abuse will be 0.