Here's what I have to say.
The Boss has already spared Matt Miller's life, but he did so because when Matt told him that he could get his empire back on track, The Boss wisely knew that the advantages were god enough to warrant sparing Matty. This shows us that The Boss is wiser in his decisions than simply killing his enemies. The Boss surely must have realised that Killbane had lost everything, including his identity if you removed his mask, and that there was no need to kill the bastard, especially considering that a top lieutenant (Shaundi) would die if he goes after Killbane. Also at stake is Viola, Burt Reynolds who The Boss is a complete fanboy of and the Saints reputation. I know that The Boss may not have known Burt was also up there and that this is not real life, but concerning the Saints reputation, they have been trying to stop it from being tarnished throughout the second it was used as leverage.
There is also a running gag that Shaundi is captured twice in both games she's been in, and that The Boss has always been protective of her. He always shows a soft spot to his allies and is not right for him to simply let them die. I don't think after Gat's death (R.I.P. lord badass) that The Boss wanted to lose another friend, and keep in mind I think the relationship between Shaundi and Gat was quite strong during the start of the game when he was alive. Just makes me think that The Boss became more concerned for her after her desire for revenge, and he may not any harm to come to her because of her close ties with Gat, and The Boss was close to Gat at the same time. The Boss left Gat to save them as always, he though Gat would be fine due to him surviving everything up until that point. Shaundi has been far more vulnerable and The Boss would recognise this, and would be more careful not to let Shaundi down, or even not let Gat down by saving Shaundi.
The achievements and trophies would suggest that Killbane big killed was the canon ending, but keep in mind anything is possible, they might have done that to simply throw us off completely. I don't think that it's a simple who lives and dies, they put two completely different endings for a reason. This is seeing how the people would react, they put in choices because of how people didn't want to kill Carlos back in Saints Row 2 and the developers decided that we should choose our ending. If the majority saves Shaundi, then the developers may have to take note on this that this is what the people want.
There may be more, something as small as Kia/Killed In Action (hint) but I still think that saving Shaundi is the correct choice. When it was said that Shaundi complains constantly even to The Boss, all she's doing is trying to do give Gat the respect he deserves. The Boss would know this and knows how dedicated she is to the Saint's, and keep in mind she must be suffering mental trauma from Gat's death, she must be thinking all the time on revenge, even Angel notices when they are Homies together. Guess you can say she's gone from always relaxing back in Saints Row 2, to now fully focus on her work and revenge.
The talk on how Gat thinks how the Saints name meant more in the earlier days, lets not forget that before The Boss became leader, the Saints were small time. Times change and Gat was still living in the early days, but The Boss helped to make the Saints evolve from common criminals to cultural icons. So the debate on The Boss agreeing that being cooperate whores is one thing, but when Kia said that she was going to make the Saints look like terrorists before saying she had Shaundi and Viola, The Boss clearly stated that the Saints are not about domestic terrorism. I still stand by that The Boss is too logical to simply deny the advantages that being international celebrities brings with it.
Looked up something on the Saints Row wiki website and just found a killer on what happened in Three Way. Shaundi's page had this written down.
"Shaundi is referenced in Red Faction: Guerilla as one of the people who left Radio Tags in the Badlands Sector. In the DLC for Red Faction: Guerilla, "Demons of the Badlands", she appears naked on a picture in the weapon stashes."
THQ and Volition are responsible for both the Saints Row and Red Faction games for publishing and development, and exists in the same universe as you would call it.
I've never played Red Faction but I've seen a Youtube video with gameplay from the game, where it shows whats on the Radio Tags and it clearly showed Shaundi's Tag (Name, photo of her from SR2).
So it's said in Red Faction: Guerrilla that Shaundi died on Mars after the Saints Row Storyline had ended and moved onto the Red Faction storyline. It has a picture of her SR2 look that proves it's her, so Shaundi, Viola and Burt must have been rescued.