This is a really unhelpful answer, but I'm going to give it anyway! My initial reaction was that "in" does sound more natural than "at". However, the more I think about it, the more "at" seems more natural. Perhaps the problem is that I wouldn't say it like this; personally, I would say something like "she's just started learning French" or "she's still at a beginner level in French". "Beginner at" and "novice at" are normally used for skilled pursuits, like archery, ice skating, using spreadsheet software, or something like that. My feeling is that using "at" in your sentences implies that she is learning French in that spirit. "In" is perhaps a little bit more neutral.

How?