ixgbe: check Core Clock Disable bit

This patch corrects the stop_mac_link_on_d3 function in ixgbe_82599 by
checking the Core Clock Disable bit before stopping link.

CC: Arun Sharma <asharma@fb.com>
Reported-by: Chris Pavlas <chris.pavlas@intel.com>
Signed-off-by: Jacob Keller <jacob.e.keller@intel.com>
Signed-off-by: Jeff Kirsher <jeffrey.t.kirsher@intel.com>