Fortunately the mistake is easily rectified, so long
as software doesn't get into the habit of expecting the lower 64 bits
of an address to be a unique interface identifier.
This is a dangerous prospect. The company I work for makes a networking
stack and our IPv6 implementation expects the lower 64 bits to be the unique
interface identifier. Other implementations do the same.
My advice would be for you and your competitors to fix this problem as
part of your normal product improvement. Because sooner or later those whose
products don't support subnets past /64 will lose business to those that
do.
It's all well and good to insist that ISPs give out /48s to their customers,
but it's not wise to pretend that everyone will comply. There will be
customers that can't get better than a /64 and will need to subnet.