On the OP situation, I agree with those who are saying the umpire should not be thinking about who "deserves" which penalty, but rather making the call based on the players actions, etc.
Go back to the modified situation that the OP wherein he stated it would be fair to call this not interference if the ball did NOT go out of play. Why would that be fair if there WAS interference?
Barring something unstated happening on the base paths (runner asleep, etc.), successful pick-off throws are usually very quick - catch and fire. A delayed pick-off sounds like an afterthought, and perhaps not an actual play being interfered with at all, just a random throw to F3.
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Tom
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