My daughter is the same age and I'd like to have the next bike I get her be one that will fit her until she reaches her full height (more likely with a 12 year old girl than a 12 year old boy, I realize).
Given that with a boy, you're likely to need at least one more replacement before he's through high school (assuming he keeps riding beyond 16), I would be tempted to get the one that fits now and just be prepared to replace the frame in a couple of years. Bikes that are too small can be made to fit with long stems and seat posts. Bikes that are too big are tough to make fit.
This coming from a guy who rides a 52 at age 39....