First thought is he might just get over it. Sometimes all it takes is time.
Somethings you can try are moving the crate. Either into your bedroom, which may help him relax. Or if that doesn't work, move him somewhere to where you can't hear him, but still keep up with the potty schedule.
Other thoughts. Do you use the crate at other times, other than just night time? Play games with the crate, leave random treats in the crate if he is out and about during the day. Basically just do anything you can to make him think the crate is an awesome place to be.
What size is the crate? If it is a big crate look into to getting a smaller one. It should be big enough to turn around and stretch out, no bigger.