According to the Grimms the verb abkommen was formerly also used in the meaning of "to agree with somebody on something":
Endlich ist mit einem abkommen so viel als überein kommen, fertig werden, sich vertragen, vergleichen. Grimm
This was similarily used like the modern verb übereinkommen which also exists as a noun Übereinkommen (agreement, convention).
Therefore the noun Abkommen indeed is a direct derivation from the verb abkommen where one of the meanings of the verb is lost today.
Interestingly it is still possible to also derive a noun from the still valid other meanings (e.g. Das Abkommmen von der Fahrbahn führte zur Kollision) but we do not use this too often, probably to avoid confusion.
Another interesting side note on this is that another noun derivation from the verb abkommen was Abkunft which today is almost exclusively used in the meaning of descent but was at times also used as a synonym for Abkommen.