I think that's a big argument for something like jQuery which takes care not to declare tons of globals or extend base classes. If the change doesn't use jQuery.noConflict() it probably should if for no reason other than avoiding any possibility of confusion when someone sees $() in code.
As for extensive customizations, how much additional concern does this add? It seems unlikely that those people aren't also using admin hacks to work around the areas which didn't used to be user-serviceable so they're probably going to need to be careful about upgrades for many other reasons. This at least gives a consistent baseline and widely-used extension mechanism for future work.