I would say the issue is already resolved. I doubt the puppy will try to take the adults food again. Since they're eating together, I assume you're feeding them at set times and that it's not a free feed situation. That's probably for the best. Besides making bathroom times more scheduled, it's usually healthier in the long run and also gives you a daily opportunity to show them that you're the provider.
I wouldn't suggest letting animals just "work it out". You could end up with one seriously hurt. I would allow them to work through it while supervised so you can step in if there is a serious issue.
Partially it'll depend on the dogs levels of social interaction. If a dog is removed from it's siblings too early, then it doesn't learn social interaction skills. That's why they say you can't take them till they're at least 8 weeks. When they play and fight with their siblings, a lighter version of what you indicated happens. One puppy will want to keep another one away and he'll growl and pounce on them to let them know. If he nips them too hard, they yelp and stop playing. That's how they learn when to correct, how to react to a correction, and how hard to correct.
A good example is my horses. Both were bred by my uncle. They were with their mother for the first 4 months and were adjacent to another mare. They bossed their mother and would rear on her back and bite her neck. She never would correct them like she should. When we let the mare in with them after a few months, both boys (1 year apart) did the same thing with the same results. The ran over, rear up and put their knees on her back and bit at her neck. She kicked them and ran off. They crept back up on her and started gumming at her trying to show contrition. She pinned her ears and tossed her head back at them twice in warning. They touched her butt anyway and got another kick and she ran off again. The next time they got too close, she pinned her ears and they backed off. When I weaned them and put them in with one of my horses, they respected those warnings too. So you can see how a lack of proper correction when they're puppies leads to issues later on.
I'm not saying that this is an issue with either of your dogs, just something to be aware of. Even if they were properly socialized as puppies, it could be that the older dog hasn't been around a lot of other dogs. If this is the case, he could have only child syndrome. If you grow up with siblings, you get used to not getting your way all the time. You realize that it's not always going to be fair or go toward you. You don't get all the attention. That doesn't happen when you're an only child and dogs can be as jealous as any of us.
It could be that your dog was just correcting the puppy the way any puppy should be corrected. It could have looked vicious but all been bluff. I had UPS drivers honking the horn for us to come out and get a package, because my old lab was raising cane. However, they could have thrown her any kind of snack and she would have helped them rob the whole house.
It could be a combination of any of these things. Here are a few options for you to try. One I'd try first is to put the bowls well away from each other and see if it happens again. I think the puppy probably learned not to try to eat our of that dogs bowl. Another thing to do is that if they act fairly comfortable, but you're worried about a knee jerk reaction, install a baby gate and feed them on either side. That way, if the older dog goes after the younger, it's blocked by a gate. If worse comes to worse, you can just feed them in different rooms. If you're not free feeding, the food bowls should come up after 15min either way, so you can put food down in the morning with them in separate rooms and closed doors in between. Get your shower or breakfast, take the bowls up and let them back together.
You can also try controlling the food. With food aggressive dogs, I've seen Cesar Milan suggest that you don't set it down on the ground. He had the owner hold the bowl of food down for the dog to eat. Then he'd have them pull the bowl away from the dog. They're much more aggressive when it's on the ground and you're walking into an area they claimed to retrieve the bowl. However, if you're offering the bowl and then removing it, it's the same as if you have a plate of food and you're giving them a pinch off your hotdog. You don't have any intention of giving them the whole hotdog and you don't. So you treat this the same way. You'll end up giving them all the food, but you act like it's a treat that you're giving them some of your intended food. You take it from one, then you let the other dog have some.
One last exercise to try is to provide the more aggressive dog with a better food if they let the younger dog eat. So if the younger dog goes near the older dogs food and the older dog starts to tense up, call their name, call them over, and give them some chicken. I think this could create a positive association between the younger dog coming to eat and rewards and good feelings.
Whatever way you choose, I don't think it'll be a long term problem. I thin if you monitor them for a week without further signs of aggression then they'll be fine. I'd also suggest that if you are, you don't free feed until you're confident that there won't be any issues. That way there won't be one while you're not watching. I wouldn't worry about the puppy either, because some dogs over react. My jack Russell has always been a drama queen. If she didn't hear me coming and I walked up and patted her butt, she'd jump forward and scream like she'd been stabbed with a kitchen knife.
I think it might have been you that posted a question about social interaction between fixed and unfixed dogs. If that's the case, then yes there is a possibility that fixing a male dog would help with guarding issues. The testosterone probably isn't helping, though fixed dogs can guard as well. Good luck.