This could be all speculation, but part of the reason for not re-recording "Put On Your Sunday Clothes" with Carol's line flub may have many reasons.
I was once told that when recording cast albums, whoever is in charge usually likes to get the Ensemble and Company numbers out of the way first, and leave the solo's and duet's (with less people) 'til the end. That way, they don't have to pay everyone the same. "Put On Your Sunday Clothes" is a company number - and not a short one - and Ms. Channing's mistake happens right in the middle of the song. Perhaps they just didn't find it necessary to record again and take up more time.
Also - the early coming-in gives us something to write about on message boards 40+ years later! And it's charming.
On the original cast recording of HOW TO SUCCEED IN BUSINESS WITHOUT REALLY TRYING, at the very end of "It's Been A Long Day", when all of the chorus comes in - there's one man who is PAINFULLY obvious singing in the chorus...in a bad way. It sounds like a they just let a janitor walk in and sing just special for this track. So odd.
During "You Can't Stop the Beat" on the HAIRSPRAY album, after Harvey's Edna spiel - the last line everyone sings before his line, "Wilbur, be a dear - fetch some oxygen...NOW!" everyone is supposed to sing "You can't stop the beat" Harvey almost flubs the line, almost saying "motion", but saves it half way through "You can't stop the moeeeeaaaaat!" I sing it that way every time.
On the recording of "Put 'Em Back the Way They Was" from Lil Abner, one ensemble member can VERY clearly be heard thinking they were at the call and response part of the chorus (when they werent) and yells "PU.." then quickly cuts off. I laugh every time.