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The choice in this is fairly straightfoward.
If you want to evacuate, then you can agree with Daniel and tell him that you'll help. This will open up some side quests and one big fight at the end.
If you want to support Joshua Graham's attack, you can tell Daniel so and the pieces will fall into place. This one works out as a long walk to the White Leg camp and then one long battle once you're inside.
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Crush the White Legs
You start off with Joshua Graham. He's your new partner, and he gives some very nice bonuses to .45 weapons. You may want to keep that in mind for the fight ahead. Note that fast travel is turned off. We've got a running battle through the valley for this one.
Follow any path you want to reach the docks right before the newly opened “Three Marys" river. You'll meet occasional groups of White Legs, so stay alert. Joshua is quite skilled though, so they won't live long. Note that the .45 pistol is practically a rifle with Graham's bonuses, and use your new skills to clear a path through to the camp.
Go down the river to join the warriors in their assault. Just watch your fire and pick off the melee fighters at the first point. Move up the slope behind this point and kill the gunner watching over the valley. There are a few ammo boxes by the chair behind the perch, if you need more ammo.
Move forward until you hit the explosion, you'll have to climb the slope and then go into Three Marys cave. I found three tribals inside. Just move carefully and gun them down as you wish. A pistol will work fine for the close quarters. Move forward and through the tunnel to reach the other side. Keep moving and then make it past the few executions you see.
The next group should be just a few White Legs before the final turn. Follow the river or go through their camps, until you hit the scene with Joshua.
You have a few options here. You can just let him execute Salt-Upon-Wounds, if you wish. You can also say the piece at the beginning, and tell him to die upon his feet. If you wish to talk to Joshua Graham, you can. You can then convince him to let Salt-Upon-Wounds die fighting, or with 90 points in Speech, you can convince him to spare him.
It's all up to you. If you choose to fight, you'll need to handle two remaining White Legs, and the very strong Salt-Upon-Wounds. He's more than a match for Joshua, so be careful. Take out his support first, so that they don't harass you while you focus on their leader. Then just pull out a heavy rifle and start firing. His powerfist is very strong, but with any luck, he'll focus on killing Joshua and you'll be able to put a few rounds in his head in VATS.
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Flight from Zion
This is actually a really short “battle." Most of the efforts are around the edges of it. If you look in your pip-boy, you'll note that you have 3 different side quests. They're spread across the map, so let's start with the closest one. You don't have to do these side quests, but doing them gives you a happier ending.
Walk forward and then up a slope to the right to approach Ranger Station Osprey. There are three White Legs standing guard. There should be a mix of shooters and melee fighters, so just move up with Joshua and gun them down with whatever you have.
You can either loot the key from a toolbox, or just pick the lock with 75 points in Lockpick. Once you set the Sorrows free, the quest will finish.
Move along the road to reach the East Fork Bridge. In order to retake the bridge from the White Legs, you basically just have to approach them with a .45 pistol drawn. Between Joshua and you, you should basically lay out a sheer wall of bullets that kills everyone on the bridge in a few seconds. Once they're dead, the quest will complete.
For the Sanctity of the Dead quest, jump off the bridge into the river and swim toward the marked bank. You should see two Sorrows waiting by the river. Talk to the one named “Dancing Flame" to learn about it. He wants to push forward and kill the White Legs on their burial mound, but he's probably a little outgunned.
With 75 points in Speech, you can convince him to just run away and forget about the White Legs. You can also convince him to just hang back and wait while you and Joshua handle it. That will buy you a little time to charge in and handle the White Legs.
There seem to be 4 melee fighters at the Burial Mound. The biggest threat to Dancing Flame will be the men with the shishkebabs. Target them first. The Sorrows should be able to handle a few with their Yao Guai gauntlets, especially if you can draw some fire onto yourself. Advance and take out the sniper, and you'll be able to finish up the quest.
Once that's done, you can move toward the Pine Creek Tunnel. Push past the battles along the road between the rear guard and the White Legs. There should just be a few pairs. Help them finish the fight and move forward until you find Daniel and Salt-Upon-Wounds.
If you have 75 points in Speech, you can convince him to just leave. The reason doesn't matter, except for roleplaying. If you pass the Speech check he'll agree to walk away.
if not, then you'll need to kill him. There are a few other White Legs around, Walk backwards and fire at them to pick them off and clear the battlefield. If any Sorrows survived on the way toward the tunnel, you can fall back to pull them into the fight and give Salt-Upon-Wounds an extra target. Other than that, just get some distance, go into VATS and put a few high powered rifle rounds into his head. He has a ton of HP, so try to VATS to take half off, then just do hit and run attacks to take him out.
Once you're finished, just use the detonator to seal the passage and finish up the game.
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After this point, you can leave Zion. You can still explore the valley as much as you wish, but the named NPCs are gone.
A bunch of custom loot is in a footchest by the exit. You can get the gear from all of the named characters along with a custom .45 pistol. You can also return to the Zion Valley later, if you wish, or if you just don't have enough room in your inventory to take everything.
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All screenshots from Fallout: New Vegas DLC - Honest Hearts