Would make more sense to software disable it? Then when new hardware comes out the older hardware can be upgraded to support a new OS and utilise the second core rather than being left behind.
As mentioned if they have switched all their 4S production over to this chip they may be able to support their Apple TV line primarily with dies that have a borked processor (otherwise those get thrown out). In that case only upgrading a portion of the people who bought Apple TVs with a software update might be counterproductive.
The simplest and most plausible explanation here is that they're using the Apple TV's relatively low performance demands as a way to get some use out of A5s with defective cores