Panic discussed this on the company blog in late 2012, outlining the steps taken to make Coda compliant with Sandboxing restrictions. The company pointed out that Apple had gone to great lengths to assist in getting Coda out the door. Unfortunately the need to get Coda in the hands of users eventually outweighed the time it would take to continue working through Sandboxing issues, so version 2.5 won’t be available via the Mac App Store.
On the upside, “switching” to the website version only requires downloading the new copy directly from Panic and installing it. That version will detect the Mac App Store version and unlock the full version, protecting the purchase you already made through the MAS.