You are right: you will sound judgmental if you approach it the way you are considering. I suggest an alternate approach, which might lead to better understanding and communication between you and your sister. Start with respect: yours of her choices, and hers of yours.
Begin with language — instead of the pejorative “married out,” why not describe him as he is — a person of a different faith, or, if he is practicing, a Christian man? By using derisive language like “marrying out” or “marrying in,” you’re creating an unnecessary rift between the two of you.
You have an opportunity to begin a conversation with your sister about her family’s choices, and about yours. You say they “do a little Judaism,” and while it’s not the same level of observance that you’ve undertaken, maybe it’s the right path for your sister and her family. Just because your sister is less observant than you are does not mean that she is “less Jewish.”
If you can bring yourself to have a conversation around understanding — not trying to persuade your sister to make different choices than she’s made—you may end up closer. Have you asked her how she and your brother-in-law made decisions around their sons’ religious education?
Maybe she and her husband had long negotiations about the children’s religious education, like many interfaith couples do. Maybe she never felt that observance was an important part of “what is behind it all.” Or maybe, she hasn’t found a community that she feels like accepts her interfaith family as they are.
If you model respect and understanding, you can then use them as stepping stones not only to nurture your own relationship, but also to begin conversations between your children and nephews that hopefully will result in your nephews not undermining your choices.
Jodi Bromberg is the president and incoming CEO of InterfaithFamily, whose mission is to engage people in interfaith relationships in Jewish life, and move Jewish communities to welcome them.