I really enjoy this feature for several reasons, and my opinion is that at most they can compromise by removing the upgrade option for brand new gear yet allow us to continue upgrading pre-5.2 gear. Some points:
-Being able to upgrade heroic 5 man gear is very useful for being able to work your way into LFR, this is of particular interest when leveling alts that you don't want to spend ridiculous amounts of gold on (and it seems wasteful spending thousands of gold on ilvl 476 epics just so you can get that extra boost to 470 to be able to do all LFR content)
-As far as alts go, most people probably want to do LFR on the first week of reaching 90, you don't want to spend several weeks grinding rep and valor capping when you already had to go through that on your main character
-Upgrading gives raiders an incentive to do more than just dailies for the coins. Some people complain that you are forced to valor cap to max your toon, however I would consider this a minor inconvenience compared to having to farm for coins and having to spend massive amounts of gold on expensive enchants like dancing steel.
-Upgrading items makes those items 'last longer', you can appreciate this now that the current system attempts to force you to change all gear each new tier due to stat inflation. You should be able to 'invest' in your favorite pieces of gear so that they are useful for a bit longer.
-Taking the option to upgrade prior tier gear out of the game is effectively removing gear, so if your lucky enough to have that 2/2 upgraded sha touched weapon or that 517ilvl upgraded heroic trinket you have something that nobody can ever get again (unless they put upgrading back in). Unless they decide to do something unprecedented and make all new items have amazing stat budgets, some people will have items that give them an advantage during a time of progression when this advantage is the most important.
I think that we need to consider a more sensible solution to the issue instead of taking the upgrade NPC out of the game. My proposal:
1. If you don't want new gear upgraded in 5.2, simply de-activate the ability to upgrade new gear until a time at which you will allow it.
2. Raise the 'floor' for upgrading gear with justice points, so that players will now be able to upgrade 5.0 tier raid finder gear with justice points, this will make it so that a newly leveled 90 post 5.2 will not feel hopelessly behind when it comes to the gear curve. This will create a 'boom' in 5 man dungeons and other justice farming activities which is great for the game overall since many people choose to get back into the game during major patch launches.
3. If you were to allow normal 5.0 raid gear to be upgraded for justice points, then players would still have an incentive to run 5.0 raids which will also be activated for cross-realm raids. This will result in more utilization of the content and an easier path for those looking to get into endgame pve. Popularizing raiding will lead to more social activity, which is at the core of keeping the community healthy.