Though at first this sounds heartbreaking (especially for me as I will in Walt Disney World in a couple of weeks), not all of Main Street Confectionary is closed. In fact, most of it is functioning as normal.
Confection Case is the part of the store currently under refurbishment and will not be open again until around the beginning of November. I would argue that Confection Case is the best part of Main Street Confectionary and is the area of the store where you can grab freshly made treats like cake pops, fudge and Mickey krispy treats.
Disney are still selling these items but if you want the experience of picking the exact one you want then your best bet is to go to Big Top Treats in Fantasyland.