My daughter had an ectopic pregnancy. If your sister's is an ectopic the pregnancy has to be aborted. My daughter had chemo to end the pregnancy: no surgery. She was about 6 weeks along.
If it's not ectopic, then the pregnancy may be in the process of spontaneously aborting anyway. I don't know what the chances of the pregnancy continuing to a successful end. It depends on what is causing the bleeding.
There really isn't any one right thing to say. Just be there with her, offer sympathy, and most of all let her talk if she wants to. Be a good listener. Don't say things like, "it's God's will", or it'll be alright. Be realistic in what you say, considering how she's feeling. This is happening. Be open and honest.
Later: my daughters ectopic pregnancy was dissolved with chemo. If tissue remained after one shot, they would give another one. It's my understanding chemo can only be done when the fetus is below a certain size/age. Otherwise it has to be surgically removed. My daughter did not mention radiation as a possibility. An ultra sound after the first chemo, in my daughter's case, showed that the tube was intact and the fetus gone. The chemicals do gradually leave the body.
My daughter is now pregnant. Ultrasounds show that the baby is developing as it should. Don't allow yourself and your sister be frightened by what might happen. Get accurate info from the doctor. In today's advanced medical world it's highly likely that she can become pregnant again if this one turns out to not be viable.