Can I call my girlfriend's sister beautiful?
It really depends on how you say it. Telling a woman that she's beautiful can be interpreted as flirting.
She just looks so beautiful that I can't resist complimenting her.
While it is expected to have a good relationship with your partner's family, it isn't appropriate to be flirty with them. Complimenting your partner's sister in that way might be interpreted as flirting, and could negatively affect your relationship. You should be cordial with your partner's family but not say anything that could be construed to be a romantic advance.
I'm deeply in love with my girlfriend and if I'm not allowed to compliment her sister then I'll never see her again because that means she doesn't trust me.
Building a good relationship with your girlfriend's family is important if you want this to be a long term romance. So it would be best if you can learn to be around her sister, but  save these types of compliments for your girlfriend.