If I remember right, Rebels never uses subtitled language, even for characters we haven’t ever seen using Basic before. But who cares! It’s your edit buddy. It sounds like a nice touch, and honestabe’s idea is a good one.
I think this was generally due to the younger target audience, and works well in that context. I also agree that a little bit of native language thrown in for flavour would be a nice touch, given the aims and direction of the project. The concept gives me Firefly vibes when they slip into Chinese to utter curses or frustration.