Late to this party...
I want to address a couple of points – and I am addressing them from MY point-of-view based both on personal experience and what I have learned over the years on this site.
First of all: Was witnessing them having sex worse than maybe learning about it some other way?
I walked in on my then-fiancé having sex with another man. Although not in any way a "good" experience, in retrospect it beats whatever I could imagine had I learned of it some other way. My imagination can visualize her having tantric, porn-star level, groaning and moaning, all-the-best-pages-of-the-Kama Sutra-style sex with a man hung like a horse, the tongue of a calf and the stamina of a Viagra-maxed porn-star. Instead, I saw two people grunting and humping.
What was happening happened. It wouldn’t really be less painful hadn’t you witnessed it, but having witnessed it might give you – in the long run – a better possibility to deal with it, accept and move on (move on as in learn to live with the reality of what happened, not move on and rug-sweep).
I don’t see that you witnessed it as some "ultimate disrespect". She never intended you to witness it – she wasn’t playing some cuckold-fetish-fantasy. You simply happened to witness it.
Yes – there is undeniably a level of thoughtlessness – even disrespect – at having sex with a close friend of yours in your house. In my experience the issue was not really that OM was in my home and in my bed. The real issue was that OM was in my fiancé.
Location certainly adds a new twist to triggers... I had to deal with serious triggers for quite some time after d-day, but when I finally had the sense of seeking professional help for PTSD part of that treatment was how to handle triggers. I guess the basement, the couch they were on (or whatever furniture) and all that can trigger you, but that is something that can be dealt with in so many ways. Key issue is that IF it’s a problem you deal with it.
I’m not making light of any of your issues. Believe me – I know you have a boatload. But I don’t see any profit whatsoever in making them worse, especially based on what WE think or on OUR moral yardstick. The Stoics said something along the lines of "a man can be as equally drowned in one inch of water as in ten feet of water". Your one-inch of issues is bad and deadly enough, without us pouring some more water on you.
Second: I would wait with sharing what happened with your son.
I am NOT much for hiding infidelity, and IF this ends in divorce OR if the affair was ongoing I would wholeheartedly recommend letting all stakeholders know in an age-appropriate way. But for now I would hold back on telling you son more than mom and dad are having issues, but that they are MARRIAGE issues right now more than family issues. That the two of you will find some resolution and will update him as necessary as far as they relate to family.
Frankly – I suspect some are suggesting you tell your son the truth more as a form to get revenge or payback for the betrayal of your wife. I’m big on honesty and truth, not so much on revenge. Nor am I big on dragging others in what really isn’t their war to fight.
I remember Dr. Phil once sharing how he and his wife had been arguing, and then one of his sons got short with Mrs. Phil. Dr. Phil took him aside and warned him that a) he never talk to his mom that way and b) he never talk to Phils WIFE that way. Keep in mind that even if this is a betrayal to you that can have permanent impact on the family, then she is his mom, and at the moment your wife.
Third: Be very clear that neither you nor your wife have any obligation to reconcile. You are in this marriage by your OWN choice. You can argue about how much D would cost, splitting the family and all that, but that’s just excuses and terrible reasons to remain married. If you want out – get out.
Same applies to your wife. You can – and should – remind her that she CAN leave for OM, and if he doesn’t want her, she can leave to find whatever was missing that she found with OM. She has NO obligation to be with you, and that if she choses to remain in this marriage it will require tremendous hard work. Work that she is committing to by remaining.
Seriously: It would be idiotic not to give divorce a very serious consideration. To the level of consulting an attorney to fully understand where you might be 12 months from now if you go that route. I fear too many claim they are "trapped" in their marriage because of [place any excuse you can imagine here like losing pension, paying alimony, splitting the family, cant afford living alone...] because they believe the mathematical enigma of divorce: Neither party get’s a fair share. In total 100% honesty I can confirm to you right now that if you are emotionally OK with divorce, you will be fine in about 24 months from filing. However – life is so much more than a financial equation, so the emotional acceptance has to be there.
Not telling you to divorce, but don’t remain in the marriage under the belief you can’t divorce. If you reconcile, it’s solely because both of you want this marriage.
Fourth: Carrying on from the divorce thoughts... This is possibly going to require a lot of life-changes anyways... Those friends are out of your life. Forever. Not for a year or two, but forever. You won’t be sending his widow a card in 30 years time, nor will you two be friends on social media. It’s a clean cut. Your basement and triggers might lead to a change in residence... Seeing as jr is 15 then maybe that was already on the 10-year schedule. Might have to speed that up, depending on if you two are married or not and if jr goes to college or whatever. Or... you manage your triggers.
Fifth and final: I am a big believer in the truth. I do think you need to know if this is the second or the gazumptionth time this happened. Was it limited to the visits, or did they meet at other times. I think that if you are left with doubts and questions on key issues then those doubts can only fester over time.
I think that getting the truth is a bit like tearing the band-aid off in one go. If you can then offer her an amnesty. If she tells you NOW and answers your questions for the next week so that you can get a sense of understanding the scope of the issue... you commit to not divorcing for the next 90 days.
Personally I would limit the questions to factual ones like: Who initiated, when did it start, how did it start, how often, did they plan, did they meet in-between visits etc. You can also clarify issues like had she had other affairs. I would omit questions on body-comparison and romantic emotions because they can seldom be answered in any constructive way.
Your 90 day commitment is only worth what you put into it. If she were to share they met every Thursday because on Wednesday’s she was doing the pool-guy... you can start packing if you are so inclined. Whatever she shares might make you leave, but whatever you discover maybe 6 months from now definitely will make you leave (thanks Sisoon!).
A key element for this honesty is her understanding that trust is shattered, and that you have reason to doubt the whole past. By being open and honest she is showing you that she trusts you with the truth, and that if you can verify that truth then it creates a base for you to reestablish trust towards her. Ask her how she thinks your marriage can ever become whole again if you don’t have that base.