I think it would be best if you took a moment tomorrow and spoke to the teen counselor. He made a bad call, meaning well. Well, and maybe with a little self-preservation built in (didn't want the actual teachers to think he couldn't handle things).
I wouldn't make a BIG deal out of it, but try to come across more as a helpful mentor.. Let him know that you talked to your daughter at length about the flower incident. And that you know he meant well and probably was a bit unaccustomed to being in that position, and not being a parent himself, he may not have realized the confusing message it can end up sending to a child when he instructs them to try to cover up something. It would have totally been ok for him to let a teacher know what was going on, and/or that your daughter was crying, and it would have all been worked out with no reflection on him. You appreciate him trying to "help" your daughter, since she was already upset. But as a parent, you recognize that sometimes it is appropriate for them to be upset. You know it's hard when they start to cry. (smile) But just for future reference, being kind isn't always the "right" thing to do, when he is an intermediary authority figure. Discussing it in private is good, and that should apply to discussions about it in front other parents and children as well, even at pick up time. Like THIS conversation. Private. But private doesn't mean you keep it from the teacher, it just means that extraneous people don't have to be made aware, because it doesn't have to do with them.
He probably just didn't know WHAT to do to comfort a crying child. And these days he certainly couldn't offer her a hug, without all sorts of accusations being potentially made against him... And then when you got there at pick up time, he was just relieved to tell you about it and get it all off his chest, not even realizing that others might hear or be listening. He was all inside his own head figuring out how to tell MOM what happened...
So just a friendly, next time you are dealing with a crying child... type conversation. Try not to be accusatory or come off as angry, b/c really, your goal (if you speak to him about it at all) is simply to help him do better in the future, right?