Kakashi is truly a genius, probably would've surpassed the 4th if given the chance to. Even without the Sharingan, he was already a perfected chuunin at the age of what... 6? Kakashi definitely has found another way to achieve Mangekyo. Itachi probably told Sasuke to do that method since it's the fastest way probably. Jiraiya DID say Itachi is rushing Sasuke. Itachi is trying to make Sasuke rush through everything. Plus, there was no way Itachi knew that Obito had died in such a way and knows every detail of the Kakashi Gaiden, therefore he couldn't have known that Kakashi was capable of getting the Mangekyo with killing his best friend. Besides... back then Kakashi had no friends because he was "emotionless". There is another way and Itachi is just hiding that fact.
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Kishi will most likely explain how Kakashi got Mangekyo... Itachi says before that there are 3 people, including Sasuke and Itachi, who is capable. Well we see 2 people with Mangekyo now and only Sasuke left... the only bearer of Sharingan left. Also, he has yet to explain the true reason what Sharingan is meant for. He left many things unanswered for a reason. So we can talk about it in forums like this for years. It's all part of foreshadowing... basic technique in all plot lines. Kishi is trying to build up the story to its peak.