Just don't put the Gateway installer on the microSD card if you are not going to use it on the target system.
It's not embedded into the kernel or anything, it's a .nds homebrew file which you can simply remove / add just like any other ROM.
As for the attempts to update the bootloader, no ... there are no updates and probably never will.
The philosophy behind it is that IF you realy want to use it on a 3DS beyond FW 9.2.0 you wouldn't buy a Gateway anyway (which comes with the blue card), since you couldn't use either.
But if you buy it for a system which is <=9.2.0, you can just install the .cia file which cearp created, to whitelist pretty much every NDS flashcard and use it on an updated 3DS (including the blue card), so I never looked any further into it.
So for the peeps who are beyond 9.2.0 I would recommend a Sky3DS (for 3DS ROMs) and any other NDS flashcard, like the R4i Gold whatever card, which is cheap and pretty much always up to date when it comes to bootloader updates for new 3DS FWs.
Or if you realy are after throwing out your moneyZ you can go for the DSTWO, which seems to be a community favourite.
I hope this clarifies the point behind our absence for the idea to update the bootloader of the blue card. It won't happen, ever
(at least not from us
)