I am one of our baby/toddler coordinators at our church of over 2000, and we see this a LOT. We even see your exact situation quite often where the little ones are fine with mother's morning out, babysitters, daycare, etc, but the nursery or class at church is a different story. Let me tell you from my professional experience that the best thing for him is for you to just keep doing what you're doing. If you know that the staff is good, then just take him and leave him, take him leave him, take him & leave him. After awhile (sometimes months...yes, I know) it'll get better and better because he'll know you're not going to just not leave him. Every week he misses going in there, is about 4 weeks back progress wise. We even have some children (with approval and conferencing from parents) that we'll leave in there regardless of the fit they pitch...never page the parents, and they are the ones that usually break through the process the fastest because they learn quickly (even the 9mth-1yr olds) that they're fits aren't going to get mommy back. About 4 1/2yrs ago, before I was a coordinator, I had a friend with a son my oldest son's age (about the same age as your son). He went through this same thing for SEVERAL months. Eventually, the teachers/nursery workers would break down and call mommy, and he knew that all he had to do was last about 10mins then go into break down mode to get his mom back. Eventually, his mom had enough, and I told her to just have them page me. So, when he'd break down, I'd get the page (we weren't close friends back then, so he didn't really know me well at that point), I'd go in there, and I'd sit with him and deal with him IN the room while he was having his little melt down, but we'd make him stay. The teachers could still do what they needed to do because I was in there to deal with him. Yes, he was a huge distraction, but only for about 5 or 6 more weeks (Sundays and Weds). It might seem like a lot, but he'd been going through his little routine for MONTHS. We've done this with several since, and it's worked.
So, if the nursery workers won't keep him in there, is there someone else that could answer the page and be in there with him? Or at least in the hall, that way you're not the one responded to his cries and letting him "win". If not, just keep doing what you're doing and give it time.
Also, you could try staying in there and leaving a little earlier each week and see if that works. Some churches don't let parents stay in the nursery, though so I don't know if that's an option for you.
It WILL pass, I promise. We're always consoling exhausted teary-eyed moms in your same situation, so it's definitely a normal thing. I went through it myself with 2 of mine and am starting to go through it with my little 9mth old princess who knows her Mommy's always on the hall working and hearing her cries. Actually, she was in one room a few weeks ago (her normal room), and one of the ladies said, "If you don't get off this hall you're just going to have to take her". So, I said, okay...What am I supposed to do? I CAN'T leave, I have to be there, I work there! So, I took her out of that room and put her in the next to oldest room because I knew they wouldn't mind dealing with her, and I was right. They got her to get her focus off the doors and windows and said to bring her in there every week, so if there's another nursery with other workers that might be willing to force him to stay in there, that would be good too.
Good Luck, and HANG IN THERE!!! The most important thing is consistency!
K.
SAHM of 4 (6,5,3, & 9mos)