L.S.
I had a kid who hated his zip up pajamas. he absolutely hated them whether he was cold or not. but when i went to regular pajamas, pants and shirt, or underoos. they stayed on. son#2 would not wear socks to bed either and he still doesn't...and he's 11 1/2.
now son #3, didn't like the zip pj's either and would take everything off but his underwear. we used boxer shorts, over underwear, and a t-shirt for pajamas and have for the longest time, and have as soon as possible. well, he doesn't like regular underwear and would only put on the boxers, with not shirt. again cold or hot. and now....he wears boxers period, no whitey tighty's on this kid. he wears a shirt if he is cold, but most times not. boxers is all he sleeps in.
if he is not having accidents, i would say he doesn't like the feel of the pajamas, they are scratchy to some people and now he can finally get them off his self.
i personally stopped using them when I realized they didn't like them. i think he is trying to tell you he doesn't like them, so i wouldn't put them on backwards.
i think i would buy some boxers and put them on over the pullup and small white t-shirts, like undershirts.
and see if he is more comfortable. or let him pick some underoos and put the underwear on over his pull-up.
i don't understand why you would make him wear the zip kind if he obviously didn't want to. and if he does sleep naked, oh well. i think in the grande scheme of things it is probably not all that important, nor a fight worth fighting. especially if he is indicating he doesn't like the zip ones. he is just trying to express himself.
i have never seen a naked kid go to kindergarten, so i am sure this to shall pass.
good luck,
L.