Essentially:

http://zero-k.info/Forum/Thread/37157

Odin targeted the unit wireframe instead of the factory itself. Thermite does very low splash damage, which explains why you thought the factory was being hit.

I looked at the replay and I'm pretty sure the thermite splashed on the factory, and that none of the caretakers were actually repairing the factory. Since the splash damage is rather low, that's why the factory lost something like 5-9% of its life (I forget) instead of being obliterated.

EDIT: Oh an you probably know this, but just so we're clear, the Odin used to have dgun. It doesn't anymore. It has been replaced by thermite, which progressively increases in damage and can be absorbed by shields, granted that they have enough health to whistand the entire duration of the thermite.