Charles' dream was one of acceptance, his desire to allow all the students under his guidance to feel that same acceptance was commendable, but the methods of the school were occasionally difficult to maintain, especially with the already distrustful street children that crossed the doors. With St John it wasn't simply a case of bundling him up, patting his head and telling him he'd be alright, Emma understood that from her first meeting with the boy, and even then he was less of a boy at the painfully young age he was still.
"Tragically I believe Charles suffers a hero complex that cannot be cured," and it was unfortunate, because for ever Scott Summers it drew in, there was St John Allerdyce to chase away. "As much as he wants harmony with human kind, he feels the need to save everyone along the way." That much was obvious from Charles' constant attempts to reaffirm things with Magneto, to smooth the way when there was no way to quell the anger in a man like Magneto.
"But there is a difference here, St John. I understand the need to feel what you do, while at the same time living how you choose. I'm the last person to throw stones about unsavory thoughts, but acting on them is entirely different. And undoubtedly, you've learned from that." Emma was of the mind that everyone learned themselves from their own decisions. She'd made her share of bad choices, everyone was entitled to do that for themselves.
"So your discomfort stems from being vilified for casual thoughts, which I assume Charles approached you about, which in turn indicated to you that he had been reading your mind without your permission?" Or St John had been projecting, but Charles would've likely dealt with that a little more subtly.