How Should I Block a Diagonal Deck?
First off, You mention the water escaping the ledger flashing - it's doesn't look like there's any flashing on that ledger board at all to me.  Is that something you were planning to add?  (I certainly would if I were you).

As for weakening the decking by moving those blocks back - I wouldn't worry about it.  An overhang of an inch or two shouldn't cause any problems.