Jonah and Amy are going so strong as of the premature Season 5 finale that it’s almost impossible to imagine how the show will write out America Ferrera’s Amy without sending Jonah too, because why wouldn’t Jonah go with her?
Jonah as a spy would definitely mean a different Superstore by the time it hit Season 5.
Assuming Amy and the others at the St. Louis Cloud 9 found out that Jonah is a spy, it’s probably safe to say that the course of Jonah and Amy’s love story would have been very different as well, if it happened at all.