Purchases from Wiiware can't be transferred to Telltale's store.
However, there is one option that you could try!
If you buy Puzzle Agent, every other item in your cart is 50% off. If you buy Puzzle Agent with Strong Bad's Cool Game for Attractive People, the order will come to $24.93, $5 less than you would have paid on its own. It's not a perfect solution, since you sank in $10 and you'll only be saving $5, but you'll pay about $25 less than you would if you were to continue buying the rest of the season on Wiiware AND you'd get an extra game out of it.
Also the Puzzle Agent deal may be ending really soon, we don't really have an end date on it other than assuming it'll end when Puzzle Agent comes out sometime this month.