It will only sound worse for the people sitting in the back. I doubt you will notice it much. You can leave the speakers in if you can make some other pass thru for the bass.
If your sure you set the gains correctly, then yes. I think you used a -3 db test signal, so you should still be able to turn up the sub out or a bass boost up to another 3 db without distortion. You can occasionally go higher, but remember your running in the red = the danger zone. Rap and hip hop music will have lots of +6 db bass notes that will push your system to it's limits.
Without having heard it, your system is geared more towards an inexpensive, but high sound quality system. If you want sheer chest pounding bass then you should have designed it a little different.
Right now the popular choice for a low cost pounding system is Fi subs and Audioque amps. Look there.
If you don't fry your gear first, you can sell it for a fair price and just pay the difference to upgrade.