The problem with bringing it up is that, if you're doing it online, the mentioning is subject to the same misconstruction.
I've been involved in my share of internet misunderstandings, and if anything, it makes it worse to say: "You may not realize it, but you are coming across as [trollish/immature/looking for offense/pot-stirring/whatever]." All that ever seems to end in is the person figuratively wailing: "The Internet is picking on meeeeee!" If there were a way to get a sarcasm punctuation mark into common use, I would be thrilled.
I think your young friend would have greatly benefited from someone IRL taking her aside and reading her comments back to her in real-time, but online? No go. In a sense, all online communication is going to be tone-deaf, including the messages that her communication style wasn't making her any friends. At least by waiting until she asked you, you could deliver the message when she was in a mind to hear it. If she wasn't, well... it's rare you can tell someone what they don't want to hear.
Example: I have a friend who I primarily talk to on Skype. He made a comment which I found sexist, and I told him to stop being a pig and think about the woman as a person, not a set of body parts arranged for him to look at. His response was basically: "but do you think she was flirting or not?" I was really angry. But on his end, he thought that I couldn't possibly be that angry, must have been joking, and was avoiding the question. My angry, to him, was Seraphia being hyperbolic and funny. His earnest question, to me, was vulgar, offensive and dismissive.
I think you did the best you could, especially since she was so young. Hopefully she learned that, in the future, humorous IRL doesn't always make you humorous on the internet.