Steven: I'd say that in applying the TDA rules you can always focus on "it's players responsibility to make his intentions clear" (Rule 2 and Rule 40). In fact, it's the only rule that is underlined in the TDA.
This means that if a player does something that's not 100% standard, it's his responsibility if you rule other than what he intended. If he truly just intended to call in your example, but you rule it a raise because of his slight of hand... that's not your fault... it's his fault.
SO, I'd just say that if you come around and you interpret his tossing 1300 and snatching back 500 to reasonably be part of the same action, then you can rule it a call.
I'd also say that I like these situations to enforce the rules rather stringently because it's a) an educational opportunity, but also b) tells the table that you are going to enforce betting rules closely. He's not out alot of $$$$, he'll be more careful next time, and everyone at the table will remember it.
But whenever something is non-standard and subject to interpretation, it's at TDs discretion, and player's responsibility.
Thanks for the great example!