Absolutely
not. (On a N3DS, anyway.) The only way out of it would be flashing a previous NAND backup, at least partially, to restore the 0x96 keystore and the FIRM partitions back to their original state.
A system update would make both your FIRM partitions technically valid, but since your keystore is still unhealthy and you've just updated past 9.6 (The exploit edits the 9.6.0 keyslot as part of the exploit), both your FIRMs will decrypt to garbage and the console won't be able to boot either of them, i.e. Brick.
O3DS would be able to survive an update (and lose the exploit with it), as stated below, since it doesn't use the N3DS 9.6+ FIRM keyslot, and NATIVE_FIRM would get replaced with the O3DS version again. That said it's still recommendable to flash that backup instead, just in case.
To be fully safe, you would have to protect the keystore (for good measure), the FIRM partitions (already done, mostly) and the 0x5C000 sector.
The corrupted firm partitions are the only firm partitions. It IS from the NAND filesystem, and there's nothing else without an SD card. Still, I wonder if there's any way to make it work like that.
Some sort of FIRM2 partition would do the trick, theoretically.