You seem to have become slightly confused in understanding what is happening in this excellent novel. Let us remember that Gitl and Shmuel are Hannah's or Chaya's uncle and aunt. Shmuel is getting married, but of course he is not getting married to his sister. Consider the following quote, that clearly tells us, and Hannah, whom Shmuel is going to marry. In this quote, Gitl addresses her brother after he has embraced Chaya/Hannah:
And go wash yourself. I wonder that Fayge ever accepted the shadchan's offer for your hand in marriage. You are so much of a prize you can kiss women without bathing?
Therefore we can see that Gitl and Shmuel are Hannah's or Chaya's aunt and uncle, but Shmuel is going to marry another woman called Fayge. This wedding of course is something that is cruelly interrupted by the deportation of this Jewish community and results in their experience first-hand of the Holocaust.