As Junior acknowledges when he comes to think about it, there is an element of truth in what Rowdy accuses him of. Although he did not physically kill his own sister himself, his actions set things in motion that led to her death. Therefore, there is a sense in which Rowdy is correct when he accuses Junior of having killed his own sister, as the following quote explores:
But she only got married so quickly and left the rez because I had left the rez first. She was only living in Montana in a cheap trailer house because I had gone to school in Reardan. She had burned to death because I had decided that I wanted to spend my life with white people.
Therefore, although Junior of course did not kill his sister herself, at the same time, he was responsible for making her want to leave the rez as soon as she possibly could, which caused her to get married much sooner than perhaps was wise, which meant she ended up in the trailer house where she lost her life. So Junior does admit that there was a causal relationship between him leaving the rez and his sister's death.