Hey mate, I'm so sorry this didn't work out like you were hoping. You must be so stressed and confused at the moment, and I imagine that you wife is feeling the same and most likely very angry at you.
I hope though, that through all this confusion and stress you feel a weight lifted off you that you don't have to hide this anymore. I know I did, but the flip side is you will see the hurt your causing your wife. It tore me up, and you question if you made the right decision. But its best to be honest with yourself and your wife, and move forward from there.
Do you have anyone for support?
It's not the best time to make rash decisions about your future now. Maybe you could suggest to her that you both commit to stay together for the next 6 months or so to work this out. Not make any life changing decisions during that time, go to counselling and discuss options for your future. Thats what I did.
You really need a LGBT counsellor and ideally someone with experience in mixed orientation marriages, I know one is Sydney that also does sessions through Skype if you need his details.
It's hard to say if your wife is using your son against you, she may well be, she's very angry and hurt, and is looking at ways to get back at you, but hopefully this will pass. But if you separate then she's thinking she will want some family around her for support, and it just happens that her family is far away.
Regardless you have rights as a father, and she can't take that away. Hopefully she can move past the hurt and regardless of your relationship with her, she will realise that it's important for your son to have a relationship with you. Not only that, its hard work raising a kid on your own, she will need the help.
Keep in mind that you have been dealing with this for 12 months or more, and your wife had no idea this was coming, and you've just turned her whole world up side down. It's going to take her some time to process. I gave my wife some space, and just got on with everyday life. And I'd let her ask what ever she wanted, but I wouldn't answer in specific details, I didn't want to say anything early on that she wouldn't be able to move past.
The next few days will be hard, I'll be thinking of you, and waiting for an update.