Mike,
First of all, I'd like to clarify TDA #44. I don't believe that it pertains to this situation. I was under the impression that "pulling in" bets was meant to prevent the dealer from "matching" a players bet with another player and pushing the equal amounts into the pot... thus isolating a raise amount or any discrepancy in amounts.
The proper dealer procedure, to eliminate the problem described in the original post, would be for the dealer to make the correct change immediately!
Example: Blinds are 800-1600. BB place two chips of 1000. The dealer should make the correct change for one of the BB's 1000 count chips by placing 600 in the bet area with his other 1000 chip, returning 400 change to the BB. It's making change as you go. I don't especially like this method but it is a solution.
Another problem I'm having with your answer is the 50% of a min raise reference...I'd like to see the 50% raise rule applied to all forms of poker but for some reason, I thought the TDA only applied it for limit poker.

The original question did not mention the limit of the game being played, but my guess is... the question pertained to no limit.
One other point to consider...the local poker room (Seneca Niagara) does not consider a raise, in no limit, unless at least 100% of the required amount to raise is placed in the bet area!
Player A bets 1000...Player B pushes out 1950 (intending to raise). The 950 is returned to Player B and he has only called!

Not agreeing, just telling it like it is. Without a prior verbal declaration of "raise" or the correct amount, it is a call.