Alright, I'm just going to say everything I want to say all at once so that I can just point people to this post every time I get in an argument about this.
So the issue people have with Touma's involvement is that they believe that it harms Misaka. They believe that Misaka is a strong female character and that having a man come in and save the day while she can only watch on is a horrible horrible thing. I want to explain why that is wrong.
1. This isn't about gender: The first argument that I want to shoot down is that this is somehow about gender, that Touma is saving Misaka because he is a man and she's a woman. He's not. This one really bothers me because Kamachi has done a lot of work to make this a very gender equal series. There are just as many strong female characters as there are male characters. To claim that this has anything to do with gender is ridiculous.
2. Misaka saves Touma's life all the time: Seriously all the time. Touma would have long ago been crushed to death, shot to death, beaten to death, etc without Misaka around to save him. He relies on her, although neither of them make a big deal out of it. He never seeks her out to join the action but she never seeks him out either, he got involved in this arc by accident.
3. Misaka doesn't just watch on: I don't know why so many people think that Misaka turns into a 'helpless damsel' in this arc, when Touma would have been slaughtered by Accelerator if she hadn't decided to get up and save him.
4. Power in this series is not linear: Just because Touma could beat Accelerator doesn't mean that he's stronger than Misaka. In this series power is much more non-linear than that. For instance Touma would get his ass kicked by someone trained in some sort of fighting style, a person Misaka would beat easily. Think of the universe as one giant game of rock paper scissors. Paper isn't 'stronger' than scissors, it just beats it due to their natures.
5. Misaka sometimes looses, but so does Touma: Yes in this arc Misaka 'lost' to Accelerator. This does not mean Kamachi is ruining her as a 'strong female character', it just means that she lost. One loss isn't that big of a deal, especially for Kamachi. Kamachi likes to let his heroes lose every now and then, he does it to Touma far more than he does it to Misaka.
6. Accelerator is not a mary sue: Believe it or not, this ridiculously powerful person is not a mary sue. Granted he's very strong, but in this series there are tons of other villains that could crush him. Yes he's much more powerful than Misaka is but a lot of characters are in this series. He also has a bunch of weaknesses that Misaka just isn't in the right position to exploit. Not to mention how complex of a character he is, which is pretty un-mary sue like.
7. This ending is a necessity: A lot of people choose to ignore this but the fact is that this arc was written for Index. It was designed for Touma to be the main character. If this was written now I'm sure that Misaka would have found some way to beat Accelerator on his own, but it wasn't. When this was written Misaka wasn't all that important. Now she is, but it's far too late to change things. If it drives you that crazy just note that it won't be happening again.
I hope that covered everything. If there's any other arguments people would like to make please let me know.
EDIT: Bonus point I forgot to add.
8. Misaka had a plan that would have worked: Misaka could have saved the sisters. If she had gone through with her plan to get herself killed and ruined the calculations then that would have worked. The only reason Touma decided to step in was because it would have involved her death.