It would stop people from using clones it prevented them from booting emunand. And if they can edit something like that out of Gateway's code, why couldn't they also edit out the supposed brick code that some hackers found? None of this makes any sense at all.
right basically gateway embedded the brick code to be basically intrinsically linked to their FW, you cant just hack it out without screwing up a whole bunch of other stuff, now seeing as the clones didnt seem capable of much more than editing strings to say R4 but not really knowing exactly what the FW itself was doing (think of it like saying "why dont you make your own game rather than a rom hack" simple answer is they dont really know what they are doing, now initially the anti-clone code was essentially what you described, if it detected a clone card it caused poor boot rates and for your saves to be randomly wiped, and the answer from clones is "back up your saves regularly and we will keep potshots until we bypass it", and everyone just carried on doing what they were doing, nobody had much to fear as long as they backup their saves regularly, if you read back over some of the threads at the time the general reaction from clone users was "trololo ha ha i get all da GW features and saved $10 and gateway can't do s*)t about it, i don't care if it takes R4 a few goes to fix it", it wasn't until the brick code that peoples opinions shifted from meh i don't care if im using a clone to "crap im not gonna get any more features all for the sake of $10" and lots of people actually did switch to gateway and tried to offload the clones onto uninformed members
the brick code was never designed to just brick everyone, it was basically guerrilla warfare, random sporadic bricks that left everyone trying to guess as to what happened for weeks, with some calling BS, others claiming it was nintendo, it wasn't until dev's stepped up and exposed the brick code, but by that point the damage was done, nobody would touch the clones, and gateway came out of it all looking like a bit of a twat, but a twat that had all the keys to the castle (at the time)
EDIT: sorry for the history lesson folks XD i guess thats enough on that subject hopefully everyone now understands how and why the brick code happened and can get over it, sure gateway did something shitty once, but they have also contributed a lot of stuff to the scene too, some people just like to try use the one thing to try make out as if they have only ever done bad