It will be up to individual nodes to decide what sources to use for these checkpoints (if any). If they rely a source that provides useful checkpoints, the effect will only be to prevent malicious chain reorganization. If they rely on some other source (or their own bad judgement) then yes they may fork their node, just as they almost certainly would if they went messing around the source code without knowing what they are doing.
You imply that the checkpoint json files will have multiple sources.
I imply no such thing, only that in distributed open source environment it is impossible to control what software people use nor what data they feed into it. I most certainly suggest people be careful where they get their checkpoint files just as they are careful where they get their software.
But if the means of deployment is just user downloading a "good" checkpoint list from official site,
well why not implement the automatic checkpointing that Peercoin has?
We considered Peercoins approach but found it unsuitable in some ways. In fact I think there are a lot of good ideas in Peercoin and often look to its solutions. I will decline to comment further at this time.