Most 'pretty magic forest' legends in actual foklore are anything but pleasant. The Fae are to be feared and revered and are fickle and petty besides. The Elementals seem to be a variation of those aspects, while still arguably a force of good as they protect the forest and the balance within - though that too can be seen as nothing but selfishness on their part as that is their home and likely their life force. To put it simply, they probably need humans in the forest so that's why we're there, and breaking the rules means we've outlived our usefulness and that's why they punish us - because why not?

I agree that while they probably wouldn't be able to harm the WoL directly, they can and will force Gridania's hand into exiling you or punishing you themselves in some other manner, and that's something the Mothercrystal can't protect you from. In that sense they're very similar to Omega - you can't protect everyone everywhere all the time, so you can't do anything but obey.