Exactly. They fled Earth because they trashed it and made it inhabitable, not because they were fat.

If you notice the scene where the pilot walks down the walk lined with past pilots' portraits, it's only after they went into space that the pilots started to get fatter, and it's a slow progression. I think this is a telling symbol. The blobbiness appears to be more a case of how those humans evolved after they left Eart.

I think this was a glaring omission on the author's part. I take his point about how society should not be equating obesity with environmental collapse, but Wall-E doesn't do that.