That has been true for every technology applied to hunting. I remember when the evil compound bows first came out. As a kid I was admonished against using a scope so I started with a peep sight. It wasn't that many year's ago when the evil crossbows were legalized in my state. When that debate went on, one argument was that "crossbows are a poacher's tool" and should not be legal.
It is not the technology, it is how you choose to use it. In my case, I use a FLIR for 3 things. Only one is even close to my ethical line; Making sure I don't spook deer when climbing down from my stand. I see no ethical issues with using it for out of season surveys as long as you are compliant with any regulations. For deer recovery, for me, it would be unethical not to use any means legally at my disposal to recover a deer I've shot.
One can use most technology in a way that violates their personal ethics. If you are "uneasy" about using any technology in any particular situation, I'd make sure you can look your self in the mirror the next day and feel good. If not, skip it. That goes for methods, technique, equipment, and such in addition to specific technologies.
Thanks,
Jack