Have you taken it to another Indy? I presume a whole transmission isn't going to be cheap so I would go to another just to get a second opinion. I'm not sure on the whole no rebuild of it because surely that would be dependant upon the extent of damage?
The symptoms provided kinda remind me of when my clutch went on my M5, bearing in mind that is an SMG so it may vary. The clutch+labour cost me £4,500 at the stealer which did hurt...
I've no idea about how the X5's transmission works but that's really all that I can say
