Are you arguing that Willpower is the most important stat and it's unfair that only psykers get access to it more cheaply?
because if so, that's silly. Many stats are important in various situations. Willpower is a good defensive stat, but the psyker will suffer other costs, because of the aptitude system. Slower move speed from less agility, take more damage, do less cool stuff with guns, etc. etc.
Yes, these can be compensated with psykik powarz, but they also cost XP and come with sweet sweet psychic phenomena.
Lastly, balance is an illusion. Especially in a narratively-focused RPG.