Harvard's introduction to CS class (CS50) has an enrollment of 651 students, while MIT's two introduction to CS classes (6.00 and 6.01) are taken by around 300 students each year.
It is possible that a larger share of Harvard students know how to program?
Probably not. A lot of MIT students learn to program in MATLAB, Stata or Java from programming classes in their engineering core (1.00, 10.10, etc.) Others come in knowing how to program and never take a basic programming class. The share of both of these groups at MIT is almost certainly larger than at Harvard. Also, Harvard is much larger than MIT, by about 60%, meaning 651/1600 students per years isn't much larger than 350/1000 taking introductory programming.
But it's still true that a surprisingly larger share of MIT freshmen can't program and a surprisingly large number of Harvard seniors will be able to by 2015.