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.