Emma R, born 1857, was a child of Israel and Hannah, according to 1860 Census in Lear River, Illinois 1870 census in Leaf River, Illinois. According to both census, sister Alice was born 1858 and is a year younger.
Emma Bethiah Alden, age 23, dau of Israel Alden and Hannah Johnson, married Milen Frederick West, age 29, Feb 5 1880 in Forreston, Illinois. She is with Milen in 1880 Census in Leaf River, Illinois. She is with Milen in 1900 Census in Leaf River, Illinois with a birth date of Jun 1858. I love 1900 Census with the Birth Month / Year. You have the Deaths Source that has the full Birth date and different death date.
So, you are correct that these sources match Emma 2. It is not the correct person for those parents. Therefore, I would remove the parents from this profile because the husband and children are correct probably. Also, the birth date of that family does not match the birth date on this profile. Part of my reasoning on removing the parents is that only this Emma's profile needs to be changed to remove the parents. If you create a new profile for the 'correct' Emma to match this husband and children, you will have to change her husband's profile, as well as all of her children.
Looking at the Changes Log, it looks like the Gedcom load for this family had her connected to these parents, as well as to her husband and children. Looking at her husband, it looks like his parents were initial this Emma and her husband, so that was a circular incorrect parent linking.
Add a Research Notes section to this Emma profile stating that you removed the parents because of 1870 (that has parents) and 1900 (that had birth month / year) census and include the Wikitree IDs of the parents. If you add a similar Research Notes section to the Parents profile, at least the father, with Emma's ID, that should stop anyone that tries to add her back as their child. At least it will be documented.
Since there is quite a few sources for the 'other' Emma, I would create that profile, link it to her parents and continue from there, at least in some sourcing that has been found. I don't find a profile for Milen West on wikitree.