Yep, it seems that the spirit liberation group just admited that they are only interested in controling people, and only have concerns for the spirits as a secondary. This is a classic example of "gain absolute control under the guise of providing protection". Its like evil scheem #8, just after "kill our own side while disguised as the eneny in order to start a war" in the "Villians Big Book of Evil Scheems". If you go with the plan, all you end up with is essentially an elitist minority run society which through their absolute control of a essential resource, subjugates the masses, turning them into slaves in everything but the name.
This guy could not have said that clearer, because if your goal was protecting spirits, then simply spreading the public awareness of what the magic stones actually are, should be enough to solve the issue.
Also, on a side note. The spirits seem to know jack shit about what they want, and seem to care even less about it. So asking them their opinion on the matter, while it is still sonething you should do, seems like a waste of time since it doesnt seem possible that they would ever give you a difinitive answer.