You can do this fairly easily with a relationship and the Go To Related Records script step.
In what format do you get your two "lists"? Presumably "list A" is a filemaker table. In what form will you receive "List B"? If you can get List B into a value list (a list of emails in one field separated by returns) you can set up the following relationship and script to do what you need:
Define gUnsubscribeEmails as a global text field in "table 1".
Define a relationship using this global field: Table 1::gUnsubscribe = List A::EmailAddress
"Table 1" and "List A" can be different table occurrences of the same data source table.
Write a Script and run it from Table 1:
Go To Related Records [show only related records; from table: "List A"; Using Layout: "List A" ( List A )]
If [ Get ( LastError ) ≠ 0 ]
Show Custom Dialog ["No unsubscribe records were found..."]
//Do what you need to unsubscribe the List A records you have found to unsubscribe
PS. a variation of this method can be used if List B is an email list that you import into separate records.