Calm down dear, its a only a one time update
Yes, Nintendo can fix this with a download manager specially for those people with slow internet. Allowing to pause and resume the downloading when you want, also allowing the background download while you play a game, etc.. Another solution could be send firmware updates throught a special free disc or included in future games as they did with the Wii. Use a compression system to reduce the file size and improve the dowload time, and split the file by parts to download them at different times.
Nintendo can use the double firmware flash feature to avoid the console brick by including a restore flash file that automatically reflash the system if the process going wrong, and unbrick the console to its normal status.