So we're to just assume that the Nero and crew wasn't held by the Klingons? Was the Klingon takeover scene in the movie on the theatrical release when it was playing? I never got a chance to see it in theaters.
No, the Klingon takeover scene wasn't in the movie - I'm not sure that any of it was even filmed.
As to whether to assume Nero & crew were held (or not held) by Klingons: we're not told anything at all about what happens to them during the 25 years between the crippling of Narada
by G. Kirk/USS Kelvin
and their arrival at coordinates for intercepting OldSpock. You could assume almost anything and the movie won't contradict you. The version that's on your DVD is exactly the same one which was shown in theaters in May 2009 - no changes were made.