To me, my penetrating stare is a gift and I utilize it often. It seems to me that you know your eyes are piercing, as you say. You also say you don’t want them to feel uncomfortable yet you wish to bend them to your will. To me, at least, these two sentences do not make sense. I think that you know what you’re doing and you’re doing a fine job (if it works) so don’t be afraid of it!
I do get what you mean. I am a polarizing person and I used to hate when I would scare people away just by being my natural self but, when one works with magic, you cannot be too concerned with this. Making one “uncomfortable” in this way already means they sense the ability in you to influence them, imo.