That's really the crux of it. People keep saying, "I just want Affleck to make one Batman movie with Reeves! I just need one film!"
Let's say Affleck did make one Batman film with Matt Reeves, fulfilling his contract. Furthermore, let's say Reeves completely knocked it out of the park. I already know what those same people would say:
"That movie was incredible! I cannot wait for a sequel!"
Too bad, because Affleck is no longer under contract.
And there's your problem. If you can't lock Affleck down for a new three-film commitment going into this, you're jeopardizing a potential Batman franchise. Don't think for one second that WB only has interest in making one Batman film, and even Reeves has hinted that he had ideas for a trilogy. It's a franchise. The studio will be thinking about the big picture. One actor isn't worth putting that on the line for, especially an actor who doesn't seem all that eager to continue.
It's better for everybody involved to just get Justice League out there, let Affleck walk away amicably, and recast the part. Simple as that.