I hope you will reconsider putting living people's information public in some format on the web. I know I would be upset to the extreme if I found out that one of my sixty cousins put my children's and grandchildren's info on the web. Fortunately, ancestry and most genealogy sites won't let you do that.
There is no such thing in FTM as making a relationship private. You can make Facts about a person private. For example, you can make the Name Fact be private and hide a living person's name. Making a Marriage Fact private does not effect the "couple" relationship that you have setup for a couple.
The focus in ancestry in making a person private or public is
1) Is the death fact filled?
2) If not, is the person over 100 years old?
3) If no birth or death date is entered, I think the default presumption is that they are dead, but I'm not sure about that. Or, you can label them as deceased or living with the radio buttons in the person's profile screen.
Your cousins's husband's family will be made public if they meet the above criteria. If you don't want them in your public tree, then create a new file for John's family and don't upload or sync it.