No. Both will be patched for sure. They never announced they were fixing the loot cave until they did it and that went on for a bit after being discovered. For the loot cave, they adjusted the respawn timers and it was that simple. It's just that this one is harder to fix, considering it's an issue inherent with the AI pathing in the game. It's not as simple as saying they could patch it the day after, they can't just band-aid it because people will find ways to break the weak fix they applied. They have to come up with something that completely prevents the cheesing from happening again, the way it is now, at least.
This might take awhile, so grab a cup of coffee.
In MMO development, there is this concept of measuring harm to the game compared to financial harm to the MMO developer and publisher. What I mean is that when you decide how to handle an exploit found by players, you have to weigh how much the game is being harmed by players exploiting compared with how much you will harm your company financially if you start banning players or rolling their characters back. If it is determined by internal analysis that you'll do more harm to yourself financially by patching an exploit and/or banning or rolling back exploiting players, you will prefer to leave the exploit alone and just address the root cause of the exploit in the next tier of content such as the new raid.
So Bungie's cost-benefit analysis goes as follows. They ideally want players to keep playing until December, and they want these players to buy the first expansion. This Atheon cheese exploit has now been available for nearly a week, although most players didn't find out about it until the weekend. Many players have probably killed Atheon using this exploit now. As the saying goes, you can't close the stable door after the horse has bolted. There is no financial analysis which suggests they should ban many thousands of players who have used this exploit, that's causing financial harm to yourself because banned players aren't known for giving you more money afterwards. Unless Bungie already has measures in place to track Atheon kills, they don't know which players killed Atheon legit and which ones exploited, so selectively rolling back characters is probably not an option.
The other issue is that they have now let thousands of players already exploit this particular bug in Atheon's AI. So now if they patch the exploit, many players who heard about it but didn't have a chance to do it will be angry when they realize that they are getting killed over and over by Vex Mythoclast in PvP and they can't get one anytime soon, if ever. The issue of when it's "too late" to patch an exploit is not a trivial one, in MMO communities late exploit patches create a community mentality of "exploit early, exploit often" to get on the gravy train right as it leaves the station and before it's derailed by a patch.
In most MMOs, exploits are monitored aggressively by the live teams and patched as quickly as possible, this minimizes the harm done to the game, it ensures only a few players are able to do it before it's patched, and so financial harm to the company is minimized because only a few players will need to be banned. Some companies purposely take the opposite stance, they care so little about harm to their own finances that they will purposely leave exploits unpatched for months so they can trap as many players as possible and ban them all later. Former players of Final Fantasy XI know what I'm talking about here.
From what I've seen, it's clear that Bungie are pretty in over their heads in terms of managing an always-online multiplayer game. They don't have the decade-plus experience of Blizzard, Sony Online Entertainment, Square-Enix, NCSoft, etc. in managing this kind of game. They should have addressed this exploit quickly after it was found, as it essentially lets you defeat the final end boss of this game's only endgame raid in about 30 seconds solo with a little practice. They have let this exploit go on too long already. So they have a pretty difficult decision to make now. They really should patch this exploit. They should have patched it within a day of it being discovered. But they have no choice now, many thousands of players have now used this exploit and if they don't patch it everybody will be using it to kill Atheon within the next week as it is now widely known and in the wild.
But there will certainly be backlash now, because the community will now be separated into players who got in on this and players who didn't, which will persist until the first expansion, the level cap raise, and the release of the new raid. The community will now be trained to "exploit early, exploit often" and furthermore they will tend to try and keep found exploits secret and passed only by word of mouth so that they won't get patched. This is unavoidable now, but the damage to the game will be so great between now and December that it has to be patched. In short, backlash or no, Bungie has to patch this. If not, everyone and their mother will be running around with Vex Mythoclast in another week or so.
Maybe that's not such a bad thing, all-Mythoclast PvP matches would be pretty damn entertaining. More entertaining than PvP is right now, anyways.