I’m so very sorry for the long delay on an answer. I’ll do my best here, but I’m sure others have covered this as well.

I think Lexa’s biggest mistake here was not taking charge immediately.  She allowed Clarke to influence ‘blood must not have blood’ and she walked away, went home to Polis and sat it out until it literally killed her.  

I don’t know the logistics for the Grounders, but if they had the ability, I would have immediately ordered all the bodies to be gathered up and placed on some mass transport system (wagons? biers?).  Since she had already ordered her army to Arkadia (that was seemingly forgotten in the episode), she could have ordered her captains/generals to have her army circle the camp, with something akin to fireballs/flaming arrows at the ready (do they have something like Molotov cocktails?). Just have them lit up, prepared to fire on Arkadia (threatening to burn it down before any Skaikru can get a shot off might be an effective threat, and they’ve got plenty of explosive material there, not to mention the immediate loss of life).  Lexa has to turn this situation to her advantage, not let Pike rest on his murderous laurels in Arkadia.  Take the fight to him, immediately, catch him off guard. She also spreads the story to her people that they have to save their brothers and sisters in Arkadia who have been ‘terrorised’ by Pike and his conspirators, setting up a redemption for Arkadia once this is all over (to Clarke’s obvious relief).

So she’s ordered her army to surround Arkadia, ready to burn it down at a moment’s notice.  She has her soldiers bring the bodies of the dead before Arkadia’s gates and lay them out, for the Skaikru to see what Pike did (if they’ve got consciences, this will affect everyone and force them to a decision about whether to support a mass murderer – a bit ironic, really).  Lexa eads this charge herself, she has to.  She announces to Arkadia Pike’s crimes, the bodies of the fallen, that they are about to burn down Arkadia, unless Pike and his conspirators are handed over.  She gives them one hour. Might be useful to have Clarke speaking to them as well, telling them to surrender (I’d never have let Clarke enter the camp, but use Octavia as a means to deliver the message, to help push the others to the right side).  

Being closely surrounded, their camp about to burn, being low on food (Pike already told us this), now aware of the deaths he caused, the Sky people will have no choice but to either give up Pike or fight to the death. Kane should be the voice of reason here, pointing out Pike’s folly, they are surrounded by thousands, on land that belongs to the Grounders, and they’ve wronged them, again, more lives taken for no good reason. Kane believes in Lexa’s fairness, knows if they surrender, the rest will come to no harm.  If Pike has a shred of decency left (he’s a ridiculous character in many ways, the school teacher who went this far without considering reality is a major stretch of believability), he’ll surrender and order his people to stand down.  The Grounders may not have bullets, but they have a righteous cause on their side and they can let Arkadia burn.

With Pike and the others surrendering, Lexa might need to cancel blood must not have a blood for a bit, since it’s doubtful the Grounders will accept banishment for him.  Pike is executed while his seconds, including Bellamy are reprimanded into Indra’s custody for their punishments (life working on farms, taking care of the families of the fallen or something similar).  

Kane, being the pragmatic leader he is, orders the Arkadia guards to surrender their weapons. This will cause controversy (and not all guns will be surrendered, obviously). They make a show of this to Lexa and her people as a sign of goodwill and Kane reaffirms their desire to remain part of the Coalition.  Lexa keeps turning this into a positive as she praises her army for their strength and compassion and saving the lives of their Arkadian brethren (using such language to keep Arkadia in the family, as it were).  She orders supplies for Arkadia to help them through the winter and offers to have hunters teach them the best places to hunt, forage, etc.  A new summit will have to go forward with new plans for how Arkadia can ‘atone’ and be a useful part of the world.

Lexa makes the point that Arkadia needs to open her gates, take down her walls in order to integrate and find peace amongst their people.  Isolation only leads to suspicion, dislike, lies and, eventually, violence.  Kane agrees (though he’s going to be fought on this by so many who do not want the ‘purity’ of their way of life invaded).  Jaha, yes, chipped Jaha, speaks to this as well, reinforced by Alie, who wants to control Arkadia for her own reasons.  

Alie, the hidden danger, decides they need to control the Commander.  To this end, she orders Jaha to seek out Clarke Griffin.

Does this make any sense? Just a few thoughts on it, but, like I said, I think others have covered this in various ways and so much of series 3 is just a narrative mess that goes nowhere, rewriting the whole thing is the only good option to make anything fit.  

Thanks for your question and your patience.