For me personally its a case of:
Do i want to see something how it was intended to look? or do I wasnt to see it as it was found?
The answer really depends on what it is..
To use Jims Halifax example, ive seen that one for real and its by far the sorryist looking thing in the room :P
As a museum peice along side other BOB aircraft that are not wrecked, Id rather see it restored as needed rather than smashed to hell. (And considering this Dornier is allegedly in pretty good shape under the circumstances)
So long as its exterior is restored with reasonable accuracy and craftsmanship -and with similar matching materials. (E.g not some crudely knocked up canopy made from mdf and clingflim

).
The fact that some of its aluminium/paint/plexiglass was manufactured in 20XX rather than 1939 wouldn't bother me much at all, the majority of it is still an orginal Do-17z
IMO, not being 100% orginal materials is small price to pay for seeing the aircraft restored to its intended appearence.
If you think about it, old cars get restored all the time, as do old buildings that are centuries old. So I dont see restoring a 70 year old bomber as sacrilege.
But after forking out £350k to fish her out, I dont know if they will have enough cash left to fix her up any time soon.....