Well, that is a nice idea, but there are a few issues.
First off, desoldering the LED/MCU PCB from the main board is a pain. Secondly, there is no reason to believe the PCB interconnection follow any standard. You may well end up with a new PCB that only works with one version.
I would rather suggest a kickstarter or something, to develop and manufacture an open hardware/software thermostat platform. Keeping it simple and cheap with only the basic and most necessary hardware by default, but with GPIO to spare to be able to extend functionality. I imagine it like a sort of a mashup of an Arduino Uno and an STC.
Yes I covered the board issues in my comments, maybe not obviously enough. Soldering is an issue for those not comfortable with it. Re-using the LED is probably a bigger issue. For my experience, this is a much simpler direction than kickstarter. Just the case parts could be a huge cost factor. Injection molds are expensive to tool.
I'm going to look at my boards and see how they compare, I have at least 3 different ones. A set of jumpers on a 'new' display board may quickly solve this.