You could try some sort of field bus.
Profibus and ASi have input modules for temperature sensors, although I don't know if the ASi ones will take thermocouples.
Perhapse Device Net or other bus system also have these types of input?
Other than that, on site here we have a lot of applications with dozens of thermocouple inputs. We wire each one back individually to its own input. The Bus systems look appealing to us for our next round of upgrades.
Hope this helps,
Doug