Just an update incase anyone comes across this thread in future!
Forks would not fit as you have guessed, they are through axle and so dont go with the disc wheels I have. I wrote an email to LBS this morning explaining really not happy, have a mismatch of a bike through no fault of my own - got a phone call from them couple of hours later, here were my choices, keep white frame, get new forks put on and new wheels all at Giants cost, or get 2016 frame (which is mostly black) fitted instead (this would be identical to my original frame/forks.
I'm tempted at this moment to go for the new fork and wheels, might not be my accepted colour but I can probably live with it for a 'free' upgrade.
Chuffed with Giant to be honest, although they could have offered to do the fork/wheels at the start without me having to complain. Happy with end result though...