I suppose it depends what he wanted to change, the gameplay or the structure. So long as the core Halo gameplay is intact, Halo can be rebuilt to be something other than a mission to mission shooter (ODST was sort of a proof of concept).
I remember in the Halo 4 panel, Frankie mentioned that they had built out a number of ideas in iteration that were great, but were ultimately thrown out because "they weren't Halo". He was making a point to emphasize how the team recognized what Halo was at its core and reassuring fans that they were going to preserve it. I don't know if these are dots that don't necessarily warrant connecting, but that's the first thing I thought of after reading the article. Put together, it sounds like Payton wanted to make substantial changes to the game that the rest of the team resisted, and so he left because he didn't feel like he could be passionate about a project in which he felt so limited.
If that's the case, his departure will be better for him, and Halo. No one should work on something they don't love if they have the choice, and Halo shouldn't be shepherded by someone who doesn't love what it is.