Sounds a little like Return to the Temple of Elemental Evil.
Instead of having positive and negative energy as their own element, instead, keep the four elements and add the positive and negative effect to those parts of the story somehow.
Perhaps during the course of realigning the element of fire. The party descends deep into a volcano, fight off some bad guy minions and then face the fire guardian. It's some beastie that serves the arch-villian and he's in charge of keeping Fire off-kilter until [the world blows up/it's time for the great ritual/the eclipse happens/etc.]
They have their fight and meet the former entity of Fire. He's weak, been drained of power by BBEG and can't hold reality together. He tells the PCs to go find another entity willing to take over. He tells them where to find some suitably powerful candidates. One might be a mighty efreet, or a red dragon, or an azer cleric, or an elder fire elemental. Basically there should be one 'good choice' and one 'bad choice' Neither choice is interested in fighting the PCs and they both are willing to accept the power. The good one promises to just keep things balanced. The bad one promises to keep things in balance and reward the PCs with power and even aid them in 'the big fight when the time comes by unleashing their powers.'
So the PCs can realign fire and move on to the next thing, or they can realign fire and receive Fire Resistance 5 or fireball 1/day, and when they fight the big bad end guy lava and flames come out the air and lay waste to his minions (of course, the volcano also erupts and destroys a town or the clouds of ash destroy crops for miles around if you're too sissy to kill people).
Same thing for earth. They solve the puzzle, choose a new elemental guardian to take over from the weakened one drained by the arch-villain, and either choose the positive option and get nothing (other than realignment of the element to buy them time or to open the portal to the End Game) or install the slightly more powerful though more wicked candidate and get some power for themselves and cracks appear in the earth that swallow up BBEG's pack of abyssal basilisks just as the fight is starting and the earthquakes knock over his hill giant lieutenants. Of course, a village is buried under a landslide nearby, a vital mountain pass is blocked off by rubble, and the nearby shaft into the dwarven mines is collapsed.
Okay, not every GM is as ruthless as me, so maybe choosing the positive option should have some rewards, but they should be less direct than the negative option, like some dwarven mercenaries show up (helpful, but it ain't the same as the earth swallowing half your enemy's army) or the PCs get metal ingots and cash from the nearby towns for getting rid of the local threat.
If the PCs travel through the raging surf and tides they can descend into the coral reef maze off the nearby coast. If they defeat the two infernal giant lobsters and the pair of sorcerers riding in the apparatus of the crab which the arch-villain has left guarding the fallen water spirit they can replace him with the 'good' spirit. Then the local port might send a naval frigate to pound the bad guy's fort with cannon fire or ballista bolts, or send a squad of marines with muskets/cutlasses/parrots/etc. to help.
Of course, if they give the power to say... the wicked marid caliph he not only realigns the element (doesn't want the world destroyed after all) but pounds the bad guy's fortress with a tsunami-sized tidal wave (that doesn't hurt the PCs, in fact, maybe he let's them breathe water for the duration of the campaign) of course, BBEG's horde of ancient fire elemental elders are extinguished and poof into steam under the assault before they get to even singe a PC's nose hair.
And who wouldn't want to see what powers the PCs get for making the arrogant cloud giant jarl into the new warden of Air? Personal wind walls to protect them from ranged attacks? The ability to air walk? How about when they reach the big fight against the evil army, the BBEG's massive dragon of bone and negative energy comes swooping out of the sky but then a tornado forms in the clouds and touches down on it just as it's about to unleash some horrific arcane breath attack. It's plucked off the ground, twisted by the tornado and snapped into pieces while thunder and lightning char and snap its bones, raining bone chips and flinging bone shrapnel into the arch-villain's goblin archers.
Of course, tornadoes and hailstorms devastate the local farms and communities and three trailer parks are lost, just plastic pink flamingo parts everywhere.
You're right that you do need another aspect though. Maybe it's the final key that comes after the epic fight with BBEG's forces, when he's retreated and is trying to claim the final piece of power. Something like 'Time'. I'm sure there's some intriguing twists and special rules you can come up with during the final encounter.
