You bridge pins 2 and 3 of u6t1 or u6t2 depending on which is installed , only 1 of the two will be. Both of them are tied to r6t3 and bridging the points is supposed to be more safe than removing the resistor. Their is a technical explanation of why on xboxhacker. Basically though if for some reason a certain part were to go bad and you only had that resistor removed it would be able to power on again , that is an unlikely if , but in any case bridging those 2 points is much easier to undo if you ever wanted to update and burn the fuses.
To answer the question , the only way really to stop it from happening is to remove that resistor or bridge the points , it literally turns off the efuse burning circuit. You can't get online with a Jtagged console so you wouldn't have to worry about an update coming from LIVE , and no you can't get online with them you get banned instantaneously i have done it. Seriously just bridge the points if you want to be safe , it is the only way other than denying the update when it asks for one , but like i said you won't be getting on LIVE with it anyways so don't worry too much about it. As an added bonus of removing the resistor , if for some reason you did try to update to 9199 it burns the fuse first so if you have that removed the update fails and you are left with a working 360 still , Before it burned the fuses after the update and you would get e80 when you would try too boot
The only thing you need to worry about is not putting a thumbdrive in thier that has the system update on it , you won't be getting any LIVE updates on a Jtagged console , and if you updated without it being Jtagged then you would lose your ability to do it indefinitely.
1 more thing to point out also , the efuses are inside your CPU die your NAND doesn't have anything to do with them , only the CPU. If it were in the NAND then every box would be exploitable by overwriting what is on the chip , or in the case of the Cygnos installing a second NAND , aka Modchip.
And i can confirm that bridging the points stops it from happening , if you didn't see the youtube video already , go ahead and do it yourself i did. Remove the resistor or bridge the points your choice , and then inssert the USB drive in with the system update. it will start then say system update failed and reboot and when it reboots everything will be fine , except if you leave the drive in it will just ask you everytime if you want too update and it will just keep failing.