If she wants to leave thats her choice it doesn't mean she gets to take your DS with her. I can't stand affairs, I just don't get it. I do understand divorce.
My XH left when my DC were 1 and 3. I learnt a lot and fast. I suggest you get reading up online and work out what YOU want. Do you want to be the resident sole parent? Shared 1 week with you, 1 with mum, alternative weekends and some holidays?
Do you anticipate you'd be living near to each other so you can both do drop offs collection from nursery etc?
The law appears to be incredibly complex around child access and residential rights. I'm a big advocate of mediation (or less formal sitting around a table with a calm person to keep focus on the agenda and points that need resolving). It is cheaper and faster than dragging things through the courts. If you can maintain a civil line of communication you'll save yourselves much heartache and your DS will benefit.
My XH was very anti mediation but his dad agreed to act as our mediator, a great man, and we each had three questions that we put to the other in advance. These were then talked through on neutral territory. Sometimes we needed to be led away from certain points to allow heightened emotions to calm down.
With a child you can never truly separate from each other if you both share access. This is just how it is. Even post 16 there are parties, graduations, weddings, birth of grandchildren etc where its in your childs interest for you to be able to behave civilly. The sooner you find a way of managing the emotion you wish to direct at her due to the situation, of her creation, the better it will be for your relationship with your DS and with her.
Talking on here can be really beneficial and help get out some of the anger/ frustration/ devastation/ confusion and blackness of the early days of shock.
Just don't forget to work out what would work for you and be prepared to negotiate.