It is more important that your kids see you happy, it is easier to parent when you are comfortably yourself. I had people tell me I should have stayed with my ex until my kids were older, my daughter was almost 3 when our court order went through. Turns out that living apart was the BEST thing for my kids because I was HAPPY and when I was happy I could parent them properly.
As for the children yes it is the parents you have to worry about not the children. One of ours is 11 right now and SHE corrects people when they call my partner the wrong name/pronoun before my partner even has a chance to. Children learn what they are taught, they can not learn what they are not taught. Right now in your sons friend's lives you may be the only one willing to teach them this lesson: "There is an outer body and an inner body." Some people think nicely dressed people are nice however, they may be abusive. A poorly dressed person might have the heart of an angel and a polite, caring nature. In the same way you teach the children these things, you will also teach them that it doesn't matter if someone looks like a girl or a boy it is how they treat you that counts.
I personally would say something to the children like this 'yes, I did let people call me my son's mom, because at the time it was easier, however I have always been his dad, so slowly more and more people are calling me his dad and it is o-kay for you to call me his dad as well.'
I hate lying and I would not be able to lie to the kids but I honestly feel that a statement like that would not be lying. Whether you were or are a man/woman you were/are his parent. It also explains enough for a child but without going into too much detail, then you can just take every question at a time and tell them it is not about appearances it is about respect. It also helps when you assure them that it is o-kay to make a mistake, to correct themselves and tell them what you wish to be called whether it be your first name or Mr. so and so.
My neighbour also has problems with children who ask her why she needs leg braces to walk, some of them are curious and some are just rude! It is up to us the people, the parents, to tell the children it is o-kay to not understand, it is o-kay to ask a question, but it is not o-kay to stare, point, laugh, or tease.
New friends take the information better than old friends and it may help if your son can meet other kids who also have parents who are not the "stereotype". I know that when I broke up with my ex my eldest daughter's best friend at the time was a girl whose parents also broke up at the same time, this helped my kids a lot. Right now we are trying to find other teenagers to talk with are oldest who is 14 and is the only one out of our crew who is showing signs of stress about the changes that have happened over the past 3 years. He is also discovering who he would like to date but that is a different issue.