Yeah, Guilt is based on the Max HP of the character it heals, not the damage being dealt.
Granted, a Faerie has relatively low HP, but it will only be held back by this, not by its low damage...
...and that said, it is a relatively low % too The Faerie may still do better not going in for this experiment. Guilt is more about helping your group as a whole sustain over a longer fight, rather than helping any individual member significantly.