Let me start by saying your son is very lucky that his mom stayed at home with him though his formative years, it is very special!
Repeating a Grade: Only you and your husband can make the choice as to whether your son repeat a grade or not. As far as harming your 5 year in the long run, not hardly, he will probably thank you for it when he is older as instead of always being the last to experience things he can be one of the first. Although I was not held back, my mother started me a year later than you could have and I thank her for that. Your son will be yet another year older and maturity goes a long way when dealing with school and other socialization skills. If he is truly smarter than the rest of his peers in the future you can always put him in the accelerated programs, versus if he continues to struggle going through the years his self-esteem will not improve and his grades and class work will keep him average.
Reason for behaviors: I am sure there are many reasons for his behavior; the newness of school has worn off. You stated that he got his tonsils out in January. During that time, I am sure that he was the center of attention, all time and effort went into his needs. Now that he is 100%, you might have eased up on the 100% attention and given some of that attention back to dad, so of course your son is not happy with sharing as that is the age. Have you talked with your husband about going back to work? Has your son overhead these conversations? It could be that your son sees changes in his life and does not want it. Children are very much creatures of routine. They work well in routines and given the chance that his routine may be shaken up a bit he is revolting, again a typical behavior for a child. Change frightens all people, however children cannot see past today, so change is HUGE in a child’s eye.
Advice:
Look at what has changed in your routine. When you have found what has changed, talk to your son about how he feels about that change. Children act up when they are fighting to gain control of their world. They want and will try to preserve that balance by every available means. It is up to you and your husband to find out what has tipped the scale of your son’s world and go back to where the scale was tipped or better yet discuss a way to move forward...always being aware that a child must move forward and things can never stay the same.
Good Luck and God Bless!
S.