He's adorable! And good for you for rescuing a dog 
So, if it scares him that much, it would be pretty hard to retrain it. It sounds like he's pretty darn scared, so I'd just drop the clicker. You don't need a clicker, and actually, you can do a mark word just the same. The reason people use clickers is all about timing, so instead you could excitedly say "Yes!" and use that as his marking word? Really, a clicker is just a tool to tell the dog the exact second he does something right.
~IJMB
So, if it scares him that much, it would be pretty hard to retrain it. It sounds like he's pretty darn scared, so I'd just drop the clicker. You don't need a clicker, and actually, you can do a mark word just the same. The reason people use clickers is all about timing, so instead you could excitedly say "Yes!" and use that as his marking word? Really, a clicker is just a tool to tell the dog the exact second he does something right.
~IJMB