In all honesty it probably will eventually. At the end of the day Nintendo is obliged to provide a safe to use system to its users. Sure, we use this exploit for save editing and the sorts, but no doubt it can also be used for more harmful means.
Compare it to Apple fixing exploits used to make a jailbreak - iOS devices are also professionally used so Apple cannot afford such a professionally used device to suddenly well... Do ... Things. Just use your imagination there.