To me, this is a clear call, in the absence of a verbal declaration. First, the 2x100 chips that the sb put in are already in the pot - the chips are no longer his to take back. In fact, in those days where the dealer would pull all the bets in after the BB's raise this wouldn't be an issue (although I know we are no longer doing that in accordance with the new recommended procedures), because the 2 x 100 chips wouldn't be in front of the player anymore to cause confusion.
In any case, when it's the sb's turn to act and it's 500 for him to call, in respect of that specific action and his option of whether to fold/call/raise he has only placed a single oversized chip into the pot without a verbal declaration, and therefore, throwing in the (extra) 1000 chip falls squarely under the Rule and is a call. I would have to disagree with the post below that if the 100 chips are not pulled back, that it should then be ruled a raise (in the absence of a verbal declaration).
I think the more interesting case that involves the pulling back of chips occurs if there actually has been a verbal declaration of raise, but no specific amount. For example, let's say the sb did say raise and instead of a 1000 chip, he threw in a 5000 chip. Would the dealer have to hold him to a raise "to 5200", or should he allow the sb to take back 200 (effectively allowing the player to make change for himself from the main pot) for a raise "to 5000"? We do see the latter a lot, and we let it go, but it would seem that this might not be technically permitted under a strict interpretation of the Rule.