You don’t have an “irrational” fear. You had a terrible experience. Memories of that experience are being triggered by men who remind you of the perpetrator when they get physically close. This is very common and nothing to be ashamed of.
You are wise not to share your history with your fiance’s colleagues. It’s not their business and it could be awkward all around. I hope your fiance can provide you with some extra support when you are with his coworkers. it’s absolutely apropriate for you to draw some boundaries around your personal space. However, as you pointed out, after three years it’s difficult to change things with this particular group without an explanation. But you can certainly be more assertive about who you will accept hugs from in the future.
The other solution to your current situation is to get into some therapy to help you separate the present from the past. I don’t see this as a “punishment for not dealing with it 15 years ago.” Instead, I hope you see it as an opportunity to put an ugly event behind you now that you are older, stronger, and able to make effective use of treatment. I expect it’s terrible to feel like your stepfather still has any power over you. You don’t want what he did to determine how you react to other people who are only being warm and welcoming, not abusive. Therapy can help you regain your sense of personal choice and power.
At only 25, you have a lot of life ahead of you. I hope you will get the help you need to have a life free from this kind of fear.
I wish you well.