As a person that haven't a got a church to go to atm, maybe I can help a little. I think that if you physically can go to church and there is a place where you feel spiritually safe, it is something we as Christians need to grow, and also to help the community. For Empaths churches can be very intense place, especially during services, because sometimes churches go through really tough times, because they grow or something isn't quite right and we feel it so keenly. I do feel that we sometimes can endure periods of not having a place to go to that is good for you, but generally it's better to go than not to.
Personally I am so ready to find a place, because since I moved and got my job I haven't had that, and I miss it, even though I never really felt I had any friends in church, the services always was very important to me.
There is alot one can do to get close to God even without a church ofcourse, and even if we have it we shouldn't rely on the services - I mean that we pray and read the bible outside of the services. In fact I think any community relies on Christians that are close to God outside of church and then come and share that with others and help each other grow.
I think you should talk to God about your situation and you'll figure it out. As far as your pain when in the church, it can sometimes as I said be a very intense social gathering.
What has worked for me in the past is that I concentrate alot on the holy spirit and Christ and pray while on the service so that I don't become so affected by the surroundings. Even praying before the service can help too. Just being very aware of God helps. Even in every day life when things happen.
I personally need to learn to do that more actually, because honestly we have the greatest helper of all, and it's a blessing to be reliant on the holy spirit for guidance and protection.