my understanding is (and I could be totally wrong here) is that if the NAND security is not lessened, it does not commit any changes to /system while Android OS is loaded. So even though it appears you can remount with rw, and you see stuff being deleted, it comes back after a reboot.
The workaround (again I could be totally wrong) is to do the modifications from adb in recovery mode. I think NAND security is lessened while the phone is in recovery mode and will allow you to make the changes. That's the reason why ROMs can be flashed with the recovery image.
I was only half-rooted via unrevoked3 for about 1 hour before simplerooting, so this is something I never tested.