For simplicity's sake, I'm going to assume by "JLA", you mean Superman, Batman, Wonder Woman, Flash (Barry), Green Lantern (Hal), Aquaman, and Martian Manhunter (the first members, basically).
Link is pretty much a non-factor here. He won't have the reaction time for any of his attacks to hit his opponents, he doesn't have access to any of his weapons besides the double helix sword while wearing the FDM, and it's hard to determine if FDM raises Link's durability story-wise, but gameplay-wise, it does not. Given the feeble things in Zelda games that can hurt Link, he would need a massive durability boost to survive against most of the JLA members alone, let alone the entire group.
On JLA's side, Batman and Aquaman wouldn't be much help in this fight, either.
Whether or not Safer Sephiroth and God Kefka stand a chance against the really powerful members of the league depends entirely on whether or not they have the endurance to survive long enough, which is harder to do (since we naturally see a lot less action from villains than heroes in video games). Assuming that they can, I'll try to play Devil's advocate:
Both Kefka and Sephiroth have the magic attack known as Heartless Angel, which puts their opponents on the brink of death regardless of how strong they are. Note that Heartless Angel works on the entire party at the same time and does not need to be casted on each person individually.
Kefka is the God of Magic and Sephiroth has impressive magical abilities from materia himself, so that puts Superman at a disadvantage. It's worth noting that Safer Sephiroth can turn people into frogs with his Pale Horse spell (since this spell works on Red XIII, it's not limited to humans).
Supernova would be a great way to exploit Martian Manhunter's pyrophobia, but it's a purely psychological attack, so it probably wouldn't do much to anyone else with really high durability if it doesn't hit them with status ailments. Since this is Sephiroth's most iconic attack, he'll try to use it regardless of whether or not he knows about Martian Manhunter's weakness. Also, both him and Kefka have strong fire magic (Firaga).
If Hal Jordan becomes confused after getting hit with Supernova (it's a possible status effect you can gain after being hit with the attack), he won't be able to use the ring properly.
The Flash can also be hit with the Slow status effect from Supernova... Which doesn't help much, since slow just halves the speed of the person it's casted on and the Flash would still be really fast with just half of his speed (also, two words: steal speed). Magic attacks in FF can't be dodged and the Flash has an average amount of durability, so maybe they could take him down...? (getting desperate here, lol)
Wonder Woman would probably be one of the biggest threats to team 2, as she is more resistant to magic than Superman and has comparable feats to him. As far as I remember, Sephiroth doesn't use his Masamune while in his Safer Sephiroth form, so that sucks for team 2. Team 2's best bet on beating Wonder Woman (aside from the previously mentioned Heartless Angel) is Kefka's Ultima spell because it ignores Magic Defense.
Final Verdict- I'm putting my money on JLA because they have speed on their side and should be able to avoid most of what Team 1 has to dish out. The only reason this isn't a stomp is because of Heartless Angel.
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