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.
Will the clients be able to deploy them in the future? That would be closer
to decentralization but then it would run against the problems with forking.
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?