So when I use my Intel Officer, he becomes "exhausted" like a defense token except I rotate the card 90 degrees. Am I then able to use him a 2nd time in the same round only I lose him permanently just like a defense token?

Page 13 of the RRG, Upgrade cards - An exhausted upgrade card cannot be exhausted again.

The main difference here is that to get the effect of the upgrade card you have to exhaust it, where as one of the effects of spending a defense token is that it becomes exhausted.

One is a cost, the other an effect.