All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad, sallallaahu ‘alayhi wa sallam, is His Slave and Messenger.
In its 29th session, the Council of Senior Scholars issued Decision No. 140 which reads:
1. It is impermissible to abort a pregnancy during its various stages except with a legitimate justification, and under very restricted circumstances.
2. If the pregnancy is in the first stage, which is the first forty days of conception, and the abortion is for a legitimate purpose or to ward off harm, then it is permissible to abort it.
Hence, there is no harm in your sister having an abortion, given her medical condition, especially since she is still in the early days of pregnancy before forty days of conception.
For more benefit, please refer to Fataawa 81706 and 87467.
Allaah Knows best.