What are the optimal methods for controlling specific header pins via Micro-USB?
There are literally hundreds of micro-controllers with a USB interface, all of which can do what you want.

Most of them have example USB software.
Some of them have built-in temperature sensors, but adding an external chip like a I2C temperature sensor is easy and also eliminates the effect of the power of the controller. 

You have to develop a tiny PCB with the chip(s) on them. 
I found writing the USB software at the PC/Android side the most challenging. 

My guess is a prototype can be made for about $100 if you do it all yourself. 
Production price greatly depends on the volume.Your biggest cost in 10-100 up volume will be the assembly house. I estimate the materials at that volume are between $5 and $10 per board.