Here's the thing: innocent until proven guilty. The OTA tunes are unlikely to cause an engine failure, but if someone stuck their fingers in and modified the tune, which then caused the failure - that's another story. The trouble is that people get wary of getting guff from the dealers over ANY mods/tunes and reflash back to the stock before bringing the car in.
So, unless you have definitive proof that someone was screwing with core tune variables to the point that the engine disintegrated - rather than simply using, e.g., Cobb maps, you can't summarily deny the service.
This just reinforces the situation in which the car owner would be more prone to denying have flashes ANY tune, perpetuating the viscous circle.