The look Hecate shared with Morgan was a meaningful one; yes, Hecate was aware Merlin's behaviour was entirely as Morgan had predicted. Morgan was right, and Hecate wanted to be sure that Morgan knew Hecate knew it.
Standing up for Morgan now though would hurt her ego. Scolding Merlin for his little jab would hurt his. All of it would upset the delicate balances of power between them all, power they needed to weave together, and ego would help, yes - having pride in ones power was useful - but animosity would not.
"Morgan is our fire," Hecate said, hoping Merlin's air was not going to fuel Morgan's fire too much. "Without her power, neither Kaden nor I would be as strong or as whole as we are today. I honour her for that, and I owe her many times over." Each word chosen with straightforward honesty, not flattery, and she looked straight at Morgan to make sure she knew that part of it, too.