I can't speak for Comcast's odd situation with WLVT and NJN there, but I know FIOS is carrying both 39 and NJN throughout the Philadelphia DMA, wherever they serve or will serve. So, Southern NJ will get 39. Fios is fully digital, so they don't have to worry too much about one local channel taking up too much bandwith.
Comcast on the other hand still has its must-carry locals on analog, which is worth 6 digital channels, and from Comcast's perspective every local channel becomes an opportunity cost consideration.
It is something unusual with WTVE 51. The Comcast cable system in the Atlantic City area carries WTVE, which is 100 miles from Reading, yet the Comcast cable system in Cherry Hill, approximately 55 miles, doesn't. I know the reason in WTVE's case is that Comcast acquired both systems, and the WTVE owner had arranged a feed with Suburban Cable servicing Atlantic City, but not with Garden State Cable. Later, WTVE didn't persist in getting carriage on Comcast in Camden and Burlington Counties - meanwhile Comcast isn't going to go out of its way to keep an analog channel for them.
Dish and DirecTV have added WTVE within the last 2 years or so, however.
For the longest time, Comcast Trenton had NJN on Ch.8, and CN8 on some other number. I think only recently NJN has been put on Ch.23 on all or most all systems, which turned to be an opening for Comcast to move CN8 to 8 there.