Is there an Enterprise version of iBooks Author?
The restrictions only apply to the .ibooks format.

From the iBooks Author Publishing and Distribution FAQ of 2/7/12:


  Are there any restrictions on the distribution of works produced with
  iBooks Author?
  
  If a fee is charged for the work and it is in the .ibooks format, the
  work may only be sold through the iBookstore. If the work is in a
  different format, such as PDF or ePub, this restriction does not
  apply.


Here's the relevant part of the updated license agreement regarding the distribution of work:


  (i) if the work is provided for free [...], you may distribute it by any means;
  
  (ii) if the work is provided for a fee [...] and included files in the .ibooks format [...], the work may only be distributed through Apple, [...], however, that this restriction will not apply to the content of the work when distributed in a form that does not include files in the .ibooks format [...]. You retain all your rights in the content of your works, and you may distribute such content by any means when it does not include files in the .ibooks format [...].