If Firewater won't S-OFF your phone with the stock ROM, then your next step would be to create a nandroid of your current stock ROM, flash a custom ROM and try Firewater again. If it's successful in gaining S-OFF, you can then restore the nandroid of stock. If Firewater comes back with the message saying it can't gain S-OFF no matter what you try, then you're stuck S-ON for now. Restore your nandroid and you're back to where you started.
If you just want to remove the bloatware and not have it return, and don't care about getting S-OFF, I believe you can flash an insecure kernel, such as ElementalX. After you install the insecure kernel, run your script to delete the bloatware and it should be gone for good.
I'm not 100% positive about this though, maybe more like 98%, b/c I've been S-OFF from the beginning and not entirely sure on the limitation of being S-On w/ unlocked bootloader. But I'm running the stock ROM, with ElementalX kernel and I've removed bloatware and it doesn't come back for me.