If a student was not showing brilliance you might say, "I would thank you for being a brilliant student" and in this sense you are asking the student for their brilliance so you can commend them. However, if the student is displaying brilliance you would say "Thank you for being a brilliant student"

*thank you for being (such) a brilliant student

I am merely explaning why we say "thank you for" instead of what you wrote. Specific prepositions follow certain phrases. The "for" follows "thank you". The gerund form of the verb "to be" follows the preposition. I am just being careful to distinguish the participle "being" I used in this sentence with the "gerund" as they look the same. The use of "such" means that the student is an example whereas the compliment is a bit stronger without the "such". Notice "compliment" with the "i" says that I am saying something good about something. It is different from "complement" when comparing things. You can also say "Thank you. I think you are going to be a brilliant student" if you are describing the future of the student.