The main reason heroes "lose their free will" is that they die (er, I mean "achieve apotheosis"). At this point, what remains of them are myths and memories, which over time, are elaborated and expanded upon by the hero's worshippers. The dead hero, like a god or spirit, has no free will because he/she does not exist in a real sense. (This is my Nysalorian-Humanist view of Glorantha)
Heroes do aquire obligations, but that is not the same as losing willpower. Heroes can "lose their will" after failing at some task, but that is a psychological effect of failure, not necessarily anything mystical. I recall that Pendragon has some rules to that effect involving Passions.
The HQ systems I've seen that subtract Will from characters are simply trying to force behaviour best done through role-playing. They are trying to enforce a campaign style where heroes go on a few great quests, then retire, either victorious or broken in spirit. In most campaigns, PCs never retire, unless the campaign ends, the PC dies permanently, or is crippled. The kind of roleplaying intensive, multi-generational games people are talking about on the digest are a definate minority, in my experience.
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