I agree with your assessment regarding Abigail Hall's incorrect parentage. Her parents were likely not William Hall & Alice Tripp, nor Thomas Hall & Hannah Cutter.
I believe her parents were Christopher and Sarah [Unknown] Hall.
(1) The handwritten original Newton town records has a section entitled "Marriages in other Towns and Cities where one of the parties belonged to Newton viz." "From Cambridge: Jonathan Ward of Newton and Abigail Hall of Cambridge were Married the 31 of December 1700 By the Reverend Mr. Wm. Brattle." [Source: Ancestry.com, Massachusetts, Town Vital Collections, 1620-1988 (Provo, UT, USA, Ancestry.com Operations, Inc., 2011), Ancestry.com, Database online.]
(2)Charles Martyn's 1925 book "The William Ward Genealogy" states that [Jonathan Ward] "married December 31, 1700, in Cambridge, Mass., Abigail Hall, born January 7, 1678." [Source: Charles Martyn, The William Ward Genealogy : The history of the descendants of William Ward of Sudbury, Mass., 1639-1925 (New York: Artemas Ward, 1925). www.ancestry.com
(3) The Concord vital records book has an Abigail Hall born "1.7.78". The record books states clearly that the clerk recorded the first month as March. So, she was born 7 Mar 1678. It is likely that the author Charles Martyn mis-interpreted the number "1" as meaning January instead of March. The Concord record further states Abigail was born to Christopher Hall. [Source: Concord Births, Marriages, and Deaths(Boston: Beacon Press), p.22.; viewable here: http://ma-vitalrecords.org/MA/Middlesex/Concord/Images/Conco...
(4) According to an 1883 book entitled "Halls of New England" by David B. Hall (available on archive.org): "Christopher Hall had a ten acre right in the town of Groton from 1660-1670; his wife Sarah, and his children: Grace, b. Nov. 25, 1672, and John, b. April 9, 1681."
[Note that author above may have been unaware that dau Abigail was born in Concord; Abigail's birth year certainly fits between the siblings listed above]
(5) Another well-known 1915 compendium states:
"Christopher Hall, the immigrant ancestor, settled at Groton, Massachusetts, as early as 1670. He married Sarah _________. He died at Groton, and his estate was administered by his widow Sarah, as shown by the Middlesex county probate records. Children: Christopher, mentioned below; Sarah, born December 4, 1670; Grace, November 25, 1672, married John Currier; John, April 9, 1681; Elizabeth (?)." [Note: even more children are listed in this family group, but still not conflicting with Abigail's birth in 1678].
Groton and Concord were communities with extremely close ties - families moved back and forth between them for much of the 17th and 18th century.
I hope this helps.