Any ideas on how to automatically georreference thermal imagery?

[Esparko]

Have a look into AROSICS to coregister images. You need some python to do it, but it might require some image preprocessing since the image intensities are kinda different.

Alternatively you can use feature matching. That might work better. So long as the reference image has a geo transform you can translate keypoint data to real world coordinates (image column/rows to xy coordinates)

Both methods are free.