It doesn't cause nearly as much confusion to the Japanese. Only the pronunciation is similar. The kanji characters are completely different, which is how it's read by those who read the novels and manga.
Misaka - 御坂
Misaki - 操祈
Nothing alike from what I can tell.
Besides, wouldn't everyone, including Kamachi, know her as Shokuhou rather than Misaki? :3 You make the argument Mikoto is referred to be everyone as Misaka, but I can't remember Misaki ever being called by her given name in the story. It's the English-speaking fans that call her that.
Japanese put a lot of emphasis on pronunciation though.
Whether people use their names to address them is really irrelevant when it comes down to comparing their actual names, and why the author picked the names the way he did. Although, if I were to say, people may use Mikoto and Shokuhou more for the mere fact that it would cause confusion if they didn't. Same goes for Misaka (clones) and Misaka (original)... it's easier to refer to her as Mikoto because you know who it is you're talking about right away, but they share the same name for a reason.
Obviously, this is all speculation... but I agree with GM when he says Kamachi has something planned out for Misaki to somehow become more important in the story as Mikoto's rival. And the likeness with the names may be a way of him to sort of hint to that.
I've actually seen this type of method done before in stories. Although, your point is just as valid.
Edited by Raijuu, 24 August 2013 - 08:48 PM.