I'm assuming the small amount that was remaining would have been no match for the Unsullied, Daario and Jorah.
Also can we now give Varys a little more credit for his actions in season 1 that, while seemed to not support Ned's cause to overthrow Joffrey, was probably more aligned with his knowledge that Stannis and his religion would not be good for the realm? I think he even had dialog with Tyrian right before Blackwater about why he's against Stannis overtaking the throne. Had Ned been successful in naming Stannis the rightful heir and casting out the Lannisters, you'd probably see an even bigger more dangerous holy war. Instead Varys opted to keep the Lannisters in power for the time being knowing that while impostors, they could still hold the fort for the time being until the Targaryan restoration was ready.
The last good look we see of the fighting pit, there really don't seem to be a lot of Sons of the Harpy left.
Also there is the Littlefinger angle. While Littlefinger likes to employ his chaos, even Stannis isn't something that Littlefinger has in mind. Even though Littlefinger essentially brought Ned to Kings Landing himself by Murdering John Aryn (had motive to bring Ned there who resembled chaos by doing the honorable thing in a world of politics), he also puts a stop to Ned overthrowing the Lannisters to put Stannis in power as the rightful heir when Robert dies. Littlefinger only plots to kill Joffrey when he knows that Stannis has been defeated at Blackwater. Now Littlefinger has gone to weaponize the Knights of the Vale to essentially take out Stannis after he has taken over the Boltons (I'm assuming that's his end game up North) & is weakened. So even players who are on the opposite sides of the spectrum( Varys & Littefinger/ Order vs. Chaos) all pretty much are in line that Stannis sitting on the Iron Throne is bad for everyone.
It isn't clear when Stannis and Mel even paired up so I don't know the answer to that question. Also, Viserys would be the one they were trying to put on the throne and he was a psychopath. Varys looks more like a Targ loyalist than a true advocate for the realm.
regarding the comments about Drogon being vulnerable. Agree with others, he's like 2-3 years old. They live decades. He's going to get 2-4 times bigger, you'd think, like the one in the Hobbit. But yet, Drogon was in trouble enough for Dany to flee with him?? If those left behind could take out the remaining Sons, then the dragon could have, too. My impression was Dany had to save him by getting him to leave, but he wouldn't leave without her, so she got on his back. Sorry, I don't get how the dragon was in trouble but, yet, there wasn't enough Sons left to finish off/capture the 4 or 5 guys left in the pit. But otherwise, thoroughly enjoyed it.
Eh... Littlefinger seems to be interested in what is best for Littlefinger. Stannis would be bad for Littlefinger because Littlefinger wants to ascend the ladder and Stannis was seen as a uniquely just individual. Rigid, stubborn and duty bound. Littlefinger taking the Knights of the Vale to the North isn't about stopping Stannis at all, it's about taking more power.
Perhaps the time that it took allowed the remaining Unsullied to storm in and reinforce Dany's merry band of men and Missandei. We don't ACTUALLY know what took place because it ended, but remember there is still another episode. It's very plausible that Drogon's attack delayed the Sons long enough that the remaining Unsullied got involved and routed them. There were only like 10-15 Unsullied in the entire arena it seemed.
Varys was getting reports back to Robert from Jorah, and that led to her almost poisoning. I don't think the Targ restoration was the ultimate plan after Robert died. It seems like he wanted Robert out at first, and then once it was obvious that Stannis was going to be put into power by Ned, then he opted for Joffrey/Lannisters. I'm not exactly sure why Varys went along with trying to take out Dany, but for whatever reason it was obvious that he did opt for Lannister vs. Stannis. He obviously at first was opting for Targaryan vs. Robert. The end result seems to always back Targaryan as an end game, but he backed the Lannisters most because he saw them as a better opponent for the Targaryans to overthrow... a more complacent infighting family. I would have to think that once Stannis was put in power after Roberts death, it would have been much more difficult to remove him, and to end the Holy war caused by putting the Lord of Light on the throne basically.
Recall that in season 1, episode 5, Varys and Illyrio are already on the same side regarding the Targaryens. Illyrio tells Varys that Khal Drogo is not prepared to attack Westeros and Varys is telling him they need to speed things up. The gist is that Varys sees a civil war coming between Stark/Lannister and that this will be a good opportunity for Viserys to be crowned while Ilyrio is telling him it is too soon. The whole almost poisoning, Jorah spying for Varys, etc. is more than likely just a plot hole. Edit: The only thing that seems possibly to make sense about the assassination attempt is that Varys didn't know Viserys was dead when he sent the order to kill Dany. Perhaps he was thinking that killing Dany and her unborn child would motivate Khal Drogo to invade Westeros for Viserys? It's a stretch, but maybe.
I don't know how it plays out yet except that we see in the preview for next week that they are alive. Perhaps the Harpies retreat from the arena once Daenarys and Drogon take to the air. Perhaps Drogon killed enough of the Harpies to give the rest of the company enough to finish off the rest of the Harpies in the arena. I suspect that with Daenarys gone there was no reason for the Harpies to continue to sacrifice themselves to Jorah, Grey Worm and Daario. Those are arguably the best 3 warriors in the city. How many Harpies would have to die in order to kill them? And no bucket of gold at the end of the rainbow if they succeed so what is the purpose? Thats my take anyway.
Remember when the Series started that Danny and Viseries were staying with Illyrio Mopatis in Pentos. We know for certain that Varys has been working with Illyrio from the very start. Tyron explained to Danny that Visaries was an honorable man but sometimes he did what he had to do, not what he wanted.
Even if she lived there is no heir to House Baratheon. Women can't continue the family name and any kids they have would have the last name of the person they marry. There probably are other Baratheons in the kingdom, kind of like Kevan Lannister.