Yes, I've had to choose between my SO and family. It's not easy and I ended up hurting both sides in the process because I chose my SO over my parents, but didn't blatantly lay it out for my parents to understand. I unintentionally made my SO feel like he wasn't worth fighting for when I couldn't overcome my fear of fighting my parents. This is tricky because I'm someone who prefers avoiding conflict.

So be sure to ask yourself:
1) Do you place more value in the end result?
...OR...
2) Do you place more value in how the conflict is resolved?

Then be sure to communicate your preference to him so that he has a better idea of how to approach the situation in a way that he can manage while also meeting your needs.

In any case, I'm glad your SO stuck up for you initially. It sounds like you're worried if he will continuing to stick up for you or not. If you think things are getting worse or feel like tensions are rising between you two, I think it's also good to consider the following:

Which is more important to you?
1) Your relationship with your SO's family
...OR...
2) Your relationship with your SO

Which is more important to your SO?
1) His relationship with his family
...OR...
2) His relationship with you

You can ask yourself, or ask him directly. Maybe even have a chat with him about it. There's no right or wrong answer to these questions. But just note that if the answers you both give don't line up...that's most likely an indication of where the problems are stemming from. Understanding where each side is coming from, hearing what he worries about versus what you worry about can help tremendously with the awkwardness.

Unfortunately until you can clear the air between you two or between his relatives, there will be a LOT of awkwardness... I hope my suggestions help and I hope you can get through this.