I suspect the answer is this: you're free to sell the e-book version for a fee and give away the iBooks version: this just makes the iPad a more attractive product and undercuts your own e-book sales. This is probably a stupid move on your part, but that's hardly Apple's problem.
But giving away the iBooks version _only to purchasers of the e-book version_ is equivalent to the iBooks version being a "feature" of the (non-free) e-book version, which is quite different than "giving away the iBooks version". This would also apply to giving away the iBooks version, but only to members of my fee-based "book club", subscribers to my fee-based newsletter, and so on. Otherwise, what stops textbook publishers from selling non-iBooks "teachers' editions" for $10,000, then giving away copies of the iBooks versions to students enrolled in courses taught by holders of teachers' editions, then passing the $10,000 cost on to students by way of "enrollment fees" or tuition hikes, offset by the fact that "textbooks are now free"?