Yes: you would use the past perfect to express a wish the past had been different, since the simple past would express a wish for the present or the future. So,
I would rather you had not told John about this
is actually a correctly formed sentence. You can see plenty of examples of sentences from published books using "would rather you had not" (or more commonly "would rather you hadn't") in this way if you do a Google Books search.
According to Cambridge Dictionaries Online, the past simple and past perfect are used with "would rather" in the following circumstances:
When the subjects of the two clauses are different, we often use the
past simple to talk about the present or future, and the past perfect
to talk about the past:
- I would rather they did something about it instead of just talking
about it. (past simple to talk about the present or future)
- Would you rather I wasn’t honest with you? (past simple to talk about
the present or future)
Not: Would you rather I’m not honest with you? or … I won’t be honest
- I’d rather you hadn’t rung me at work. (past perfect to talk about the
Incidentally, the BBC also discusses the use with the simple past that you show in the example sentence in your question:
Would rather (but not would prefer to) is also followed by a past
tense when we want to involve other people in the action, even though
it has a present or future meaning. Study the following:
- Shall we go out for dinner tonight? ~ No, I'd rather we ate at home,
if you don't mind.
- Shall I write to Harry and tell him that we've sold
the car? ~ I'd rather you didn't.
- My mother would rather we caught the bus, rather than walk home after the party.