Long before I was a Pony fan, I was a fan-fiction writer. I make no claim to any special skill or insight but I have my own ideas about how I would have handled the final confrontation with Starlight Glimmer. This is my idea in summary:
I would have had the entire Mane Six pulled into the time vortex when Starlight goes back in time to alter history. After some initial confusion, they engage Starlight at the Young Fliers camp and take her out on the first attempt, capturing her after a high-SFX battle with her throwing every magic trick she knows into the game. Unfortunately, they were too late to stop her altering the events of that day. Despite their best efforts, Starlight's spell dodges all their attempts to block or dispel it and hits filly!Rainbow, preventing the Rainboom.
The Six, Spike and their prisoner are dragged back to the present to an Equestria in the middle of a four-sided war between Sombra, Nightmare Moon, Celestia and the Changelings. Worse, Discord is hovering around finding amusement in further aggravating matters by inducing 'artistic' little bouts of localised chaos. That's when the real saving grace of the episodes, Resistance Leader Zecora makes her appearance. The Six make a few attempts to help the 'good guys' but it is painfully clear that, even with their superlative abilities, they are just a tiny light on an onrushing tsunami of darkness.
The Six arrive back at Zecora's hidden fortress deep in the Everfree, talking about how the Rainbow Power was able to drive away Sombra's dark magic but how it wasn't destroyed. Twilight theorises (as Starlight Glimmer, currently hobbled and with a magic suppressing cap on her horn, mocks them from the sidelines) that it is due to the fact that Sombra has so much despair, rage and pain on his side and there is so little of the qualities of the six Elements being felt in this version of Equestria.
The episode thus ends on a serious down-note with our heroines wondering if they can win this time.
Zecora helps them interrogate Starlight with the help of a truth potion. Starlight explains how her spell works; that, after casting, it will always home onto filly!Rainbow because it is magically bonded to her aura and can only be dispelled by she herself. She also explains the scroll spell has created a bubble of 'protected time' around everypony who went through the time warp. However, when that spell finally degenerates, they'll all merge into the ponies they would be in this altered time-line with no memory of the original. Naturally, she doesn't care about the broader problems, so long as she was still the total overmare of her idea of a 'happy' Equaltown.
Zecora reacts with interest to Starlight's description of 'her' town. She explains that it was the first place Sombra trashed when his forces crossed the Icy Mountains into Equestria proper and that its leader is now his court jester; who knows what he has done with the rest of the slaves he seized that day...? Starlight has an immediate Villainous BSOD.
Zecora tells them that they have to go back in time and ensure that the original time-line is preserved. There follows a series of adventures as the Mane Six try to find some way to undo the harm as the jittery time-spell drops them off separately in various points in the past (including Starlight's fillyhood, where Twilight, Spike and Starlight witness Sunburst's painful moment of destiny and its affect on young Starlight). There is a moment of heart-warming as Twilight comforts a crying present!Starlight; you get the impression that it is the first time that she's really expressed her emotions arising from that day.
Finally, with all other options exhausted, they converge on the Young Fliers camp. However, past!Starlight is skilled and determined; she keeps on burning her way through traps and using what could be considered lethal force. Her spell, when launched, dodges barriers and burns through shields with ease, At the very last moment, present!Starlight breaks loose from her bonds (she'd been working her way loose for a while and we've seen hints of this) and throws herself into her own past self's magical attack. The resulting paradox creates a huge SFX feedback loop. The two versions of Starlight merge and her magic fails, causing her to plunge through the cloud to her doom... if Twilight didn't dive down and catch her. Twi rejoins her friends just as filly!Rainbow breaks the Rainbow Barrier and creates the first Rainboom.
Epilogue is in the Castle of Friendship. Starlight explains to Twilight that everything she did was for what she perceived to be the best interests of the ponies of Equaltown. Blocking the spell with her own self was the only way she could think of protecting them from the horrors of the war-torn alternate time-line. She then asks Twilight why she saved her life. Twilight responds that it was the right thing to do and she encourages Starlight to make new friends. Destinies do not have to pull ponies apart if you do not wish it to - She cites her efforts to make peace with Moon Dancer as proof of this. She points out that the loyalty that Starlight had shown to those she once ruled over could be considered 'friendship' too.
"So, how about it? Are you up for making some friends?"
"I... don't know how to."
"I'll show you."
End as in canon with it very clear that Starlight has gone back to Equaltown, a place that is special and dear in her heart to serve her penance by helping the ponies she once tyranised. There is something very odd about the way she and Double Diamond hug... (wink)
What's The Point?
The real underlying point is two-fold.
Firstly, we start Starlight's redemption a lot earlier in the story, actually at the beginning of part 2. By the climactic sequence, the following has happened:
- Starlight has found out that by changing the timeline, she has caused the destruction of her 'perfect society' in Equaltown's even earlier than the original timeline!
- Starlight has seen the Mane Six fight, not for their own friendship or their own selfish interests, rather very explicitly for the good of all Equestria, even when all hope seems lost';
- Starlight has had the chance to talk about how important Equaltown and the ponies there are to her, establishing a secondary motive beyond her fillyhood trauma;
- Instead of clinically dissecting her own pain or even mocking it, Twilight showed her empathy and extended a hoof of sympathy and comfort, even though she had tried to destroy her.
So, it would make sense for Starlight to make a Face Heel Turn. She's seen that there is more to the Mane Six and their friendship than their happiness; this is a group of ponies whose nature, as amplified by their friendship, is something worth emulating.
Then, we have her attempted 'Death equals Redemption' act, which I think would have settled in all the fans' minds whether she deserved forgiveness.
Secondly, instead of having multiple alternate futures, we have one distinct one, thus being able to establish it is a dark alternative a lot more clearly and even have more focussed interaction between the Mane Six and this alternate world. This solves the pacing issue and allows for a more focussed development of the main character arcs and plot.