Well, that wouldn't bother Balanchine any. Suzanne Farrell said in her book that he loved to partner her in rehearsal even though she was quite a bit taller than he when she was on pointe, and in fact the height differential helped their partnering. ("Look how we fit together," he'd say. Subtle.)
Le Clercq was always called coltish, as she noted herself, and she was indeed considered quite tall and angular for the time. By today's standards her outline is rather soft; she's more curvy than you would think from contemporary descriptions. Fashions in bodies, particularly women's bodies, tend to change over time. Pavlova was considered almost dangerously thin in her day, but she doesn't look so to us.
A digression: I remember reading that the late Nelson Mandela told a Western reporter that she was too thin, and in his young day they liked women with more meat on their bones. I suppose that was sexist of him but I'm sure he meant well, and it's a remark any dieting woman should appreciate.
I like that word "coltish", and what it connotes. It's interesting to me how the preferred female form has changed through the years and in different cultures. Paintings from the Renaissance period show women that are rather heavy by today's standards, but back then, such figures were a sign of being well fed, something that wasn't taken for granted the way it is today. One of Balanchine's other muses was Maria Tallchief. I've read she was a whopping 5'9, so I'd say you're right, Balanchine wasn't bothered by it. I saw film of her next to Le Clercq, and there didn't seem to be a huge difference. Maybe Le Clercq was 5'7?