I still don't get it. Can't you just pay off your deck next turn before buying any cards? You can pay off debt both before and after buying cards, right?
Next turn you won't have whatever money you have sitting around this turn.... Let's say you have no money at all, and go to your buy phase. You play Capital. Now you have $6. You buy a Smithy. Now you have $2. When you discard Capital from play, you take 6 debt. You immediately pay off 2 of it with your leftover money. Now you have 4 debt.
Without that clause, you would start your next turn with 6 debt instead of 4, and you would have wasted $2 of the $6 that Capital gave you. Basically, the clause allows you to borrow any amount up to $6; without the clause you would have to borrow exactly $6.