It's really not a good idea for you to try engaging your ex at your son's games. It is stressful on your son, and totally unnecessary.
I like that you have tried e-mailing her to address the wedding situation. But, JMHO, you've waited way too long. I'm sure you know how much planning is involved in a wedding, and I can see where she would be frustrated with not knowing whether or not her son would be in the wedding. Granted, she could have scheduled it during her weekend, but sometimes scheduling doesn't work out the way you want - and you hope the other side will work with you. She's probably super stressed out at this point and doesn't want to deal with anymore changes.
Option #1 is good. However, your language is a little antagonistic. It feels like you're saying she's making a big deal out of nothing. It might have been better to say something like: "Son would like to attend your wedding, and I think it's important for him as well. I am offering for you to have him during my parenting time so he can attend the wedding. I would like to get make-up time in return, which we can discuss when you return from your honeymoon. Please let me know if you want to have him so I know if I need to pick him up or not."
Option #2 is a little silly because the last thing someone wants to do on their wedding day is deal with custody exchanges with their ex. I'm sure you can understand why.
It's a little late for anything at this point because her plans are probably set. I doubt that she's going to want to deal with it at this point, and I honestly don't blame her.
I'm a firm believer in picking your battles. Weddings are major life events and I think, for your son's benefit, that both sides should put down their swords and calculators and do what's right for the kid. He's missing a big event - where he could bond with his family, and also take a big step towards adjusting to his mom's new marriage. Being included is good for the kids because it helps them not feel like the parent is starting a new life without them. Your son deserves that security.
Like I said earlier, sometimes you have to stop worrying about what the other side is or isn't doing, stop waiting for them to "get what's coming to them", and just do the right thing for your kids.