Destiny is one of the Three Virtues valued in the Bionicle Universe.
While Turaga Hakari does not doubt the validity of the Guardian's legend, he does doubt its accuracy. The Guardian sees prophecies by seeing into Destiny, which is a very real and very powerful force in the official Bionicle storyline. Destiny doesn't always come true, and when it does it isn't always in the ways that it says it will. This is particularly true for the comic land. Hakari may just think that prophecies are less accurate than weather forecasts and are unreliable. Agni, the leader of the neo-ninja (the one in the Kakama Nuva up to the left of the toa), thinks the same way.
Even in the official storyline events of the Bionicle canon, Destiny is ignorable and changeable. An example of this is the Bohrok being released early.
On top of all of this, The Guardian's personality traits seen in the movie only made up for a small fraction of his sum total personality. Fact is, The Guardian was known for having a very eccentric and forgetful personality when not in a serious situation. He was wise and all that, it's just that sometimes people wondered if he wasn't the brightest match in the box. Turaga Hakari must have been thinking how can an old legend thought up by some famous old dead prophet with such a complex personality using such an unreliable force to guide him be trusted?