After doing a bit more research, I now believe that Maybee Barnes was the son of Thomas Barnes from Middletown, and that Thomas Barnes of Farmington was indeed a different Thomas Barnes.
On the NEHGS website, in the Early CT Probate Records, I found two wills:
Thomas Barnes, (Sen) of Farmington (Vol 1, page 402) will date Jan 9, 1688, mentioning his wife Mary. It refers to her as his "sd." wife, not sure if this means second or stated? Also mentiones a son Thomas, Ebenezer, and other children "already gone from me and disposed in marriage". John Hooker of Farmington and John Stanley sen. both witnessed the will, and it was approved by the court on March 6, 1689/90, after Thomas Barnes' death (he died sometime before Feb 7th of 1689/90, based on John Hooker's oath of that date). This would be the THomas Barnes who made the contract on March 23 1662/3 with John "Androos" to marry his daughter and stating how he will provide for her on his death, and "putting out" all his children except Benjamin and possibly Hannah is his wife will allow her to stay.
Thomas Barnes, sen. of Middletown made a will (Feb 25, 1683?) which mentions his eldest son John, sons THomas, Daniel and Maibe, daughters Mercy Jacobs, Martha, Elizabeth, Abigail. Witnessed by Daniel Harris, jr. and John Hall, Sr. On Oct 6, 1692 John Hall swore that Thomas Barnes was of sound mind at the time of his will being written, and on Sep 7, 1693 the will was proved and recorded. The will does not mention his wife by name.
So, it looks like Maibe was not the son of Mary Barnes of Farmington who was burned as a witch. The Thomas Barnes of Middletown would be the one who signed the Colony Constitution in 1644. In the "Families of Ancient New Haven" (p.90) Mary Barnes is given as the mother of Elizabeth Barnes, who married John Austin, though I am not sure whether Eliz. Barnes birth/baptism date are correct. On p. 323 it lists the marriage of Benjamin Brockett to Elizabeth Barnes on 24 Mar 1668/9. All of this info is supposedly from the New Haven Vital Records.