Remember that the agreement that Fry and Leela should get together comes after everyone knew that season four was the last one. So I'd take it more in a wrapping up the overall storyline way than just an individual episode or permanent story change (cf the death of Maude Flanders in The Simpsons
) in an ongoing story arc. Especially as the reference is to a ninety minute program (ie a TV movie rather than a regular episode) which a lot of long-running series wrap up with if they get the chance.
As I have tried to stay away about from mentions of plotlines and just general spoiler-like stuff about the three remaining movies I'm not too sure how reliable this is but I understand that the last of the four movies (Into the Wild Green Yonder.)...
is going to contain something like a resolution to the Fry-Leela story line.