I too have a 3 yr old boy, who was somewhat trained to go "pee" on the potty around his b-day in june. He was going to a summer preschool program and had to be potty trained. He went to the bathroom to pee with no problems or accidents... but he would not sit on the potty to "poop". I had him playing outside (bare bottom) and i brought the potty seat outside in case he couldnt make it into the house. Again he would pee sitting on the potty, but would hold his poop. He pooped twice, just standing up and it fell to the ground. (Yuk - i'm sorry) I thought that maybe he didnt want to sit to "poop" ???? I had no idea...
Fortunately, he could hold it and he would tell me "mommy, i am a little tiny baby and i need a diaper to poop" I would put a diaper on (we still use them at nap and overnight)and he would poop, then I would take it off right away and we would dump it in the toilet and flush etc...
When he would tell me he wanted a diaper to poop I would first put him on the toilet to see if I would get lucky with timing and he would feel what it felt like to go on the potty and not be scared... he would just cry and like you I did not want to traumatize him.
Again, I was lucky because he would not poop in his underwear, he asked for a diaper. Since he wore underwear to preschool, and it was only a couple hours, he would wait until he got home and poop in a diaper.
after a while he would poop maybe 2x a week on the potty, but request a diaper all the other times. he would also wait until nap or bedtime when we put a diaper on to go. I just went with it, because he actually had himself on some sort of schedule :-) He would also poop in a public bathroom if we were out for a long time running errands or at a restaurant. I guess he knew I did not have a diaper and he really had to go. Eventually, he became less and less scared of popping on the potty.
Now he poops on the potty all the time and asks for a diaper 2x a week. boys are harder. I think he was scared and it was a control thing with him too.
Maybe try telling him that if he lets you know when he has to poop you will put a diaper on etc... Then you will both have a little more control... Seems like yesterday that i was wondering why he wouldnt sit on the potty to "poop" and now 4 months later he is almost 100% trained. soon it will just be a memory. :-)