I would do it and would never even think twice about it. I am privy to every rep chargeback and regional warranty specialist decision, but I have never seen a chargeback solely for a shop performing a cross-line repair.
If you want protection, write the story as you have it. It doesn't fall into one of the defined categories - unless you stretch and define the "emergency" as being the customer didn't want to drive a vehicle with a miss any further.
But believe me, there are many stores doing much much much more than this and nobody has ever raised the issue to them. Most reps I have ran into lately probably don't even know what the crossline restrictions are.