I faced with AD limitations on my work and the best solution i choosed - use MSADHelper.dll by Igor Kovalenko.

http://blogs.msdn.com/b/ikovalenko/archive/2007/03/22/how-to-avoid-1000-rows-limitation-when-querying-active-directory-ad-from-sql-2005-with-using-custom-code.aspx

It works perfect.