Is there anything that can be done to allow me to protect my images while using thickbox outside of manually adding an actual watermark onto each image using photoshop. If not, are there any alternatives to thickbox that would allow it?

It is a limitation to Thickbox/Js that it needs the unprotected full image. I don't think it will work with any other JS. But you could try to open the protected page via the iFrame option of the thickbox. Have not tried it though.