You said that you can't run it deferentially, but I don't see why not if you're adding a new sensor with new wiring and new signal conditioning. You are not obligated to ground one end of the thermistor near the sensor just because that's the way some auto manufacturers do it. You can do whatever you want!
As I mentioned above, some IAT's ground one side through their mounting bracket. We could require an insulating mount, maybe....
But yes, I'm starting to think that we force some changes back upstream. Possibilities include:
1) Require both sides of the sensor to be electrically isolated so we can do what we want (no manufacturer-grounded sensors)
2) Just package our own sensor in our device, and require that they mount our device at the desired sensing location. This keeps all our stuff tight and compact. All we need is +12V, Ground, CAN-H, and CAN-L which are far more noise tolerant than a thermistor at the end of a long harness run.
I'm leaning toward the latter because it puts us in control of everything. Standalone thermistors are ~$0.40/100's so this might actually SAVE them money in the deal as compared to packaged IAT's which appear to be several dollars and up, plus requiring a mating connector.