Look at it from the point of Nicholai. They manufacture in house unlike the big brands so are pretty sure of the quality of the product leaving the factory. Being German engineers, you can be sure that the QC is pretty rigorous and I bet they are convinced that a deformed frame would never slip through.
Some one buys a frame and rides it with no issues for the best part of a year and only then starts making complaints about a misalignment. The fact that he claims not to have ridden it much is not exactly easy to prove (he might even have taken it abroad and had it chucked around by cargo handlers etc). All they know is that is has taken a VERY long time for the customer to complain about something that should have been apparent very quickly if it had been a manufacturing issue.
Replacing for free might have been the best in terms of PR but its one of those commercial decisions. You believe the bike left the factory in good shape so why lose money (that a small company can ill afford to do) to placate one customer who in your view is probably chancing his arm. Nicolai UK is unfortunately just caught in the middle so you cant really blame him.
I guess the brands that subcontract their manufacturing are more inclined to replace stuff as they just pass on the loss to their manufacturers and it costs them nothing.