I am not so certain the Mogmas are mischievous as they are protective. Remember they are living down on the surface that is said to be dominated by evil with a Demon Lord presiding over it. They do not have the protection of the gods to lift them into the air for safety so they have to find security through other means. By hiding deep within the ground and living near inhospitable areas such as volcanoes. And of course a Hylian might look exactly like whatever tribe Ghirahim hails from so they may not know the difference. One pointy eared human is just the same as another to them, so they would take steps top protect themselves by breaking the key and running away. That would keep whatever encroaching evil out of their lands temporarily. At least in their minds it might.
And all this talk of evolution, Wind Waker really threw everyone off with the Zora/Rito evolution. Now it seems that each time a new tribe is introduced it is genuinely assumed that they must have originated as another known species first. Before becoming the new totally unrelated species we see today. I really do not think they are in any way related to Gorons, we have seen other subterranean tribes before in other games that were not Gorons. The Subrosians live deep within the earth as well, even fairies are commonly found deep in caves. If there can be multiple tribes that live in frozen lands(Anouki, Yook, Yeti), within the water (Zora, River Zora, Fishmen), in the desert (Gerudo, Zuna, Cobble), and in the forest (Kokiri, Deku, Monkeys), and even the sky (Rito, Oocca, Wind Tribe) then I do not see any issue with having multiple tribes that live underground as well.