The reason they rated Kurt in front of EVH is because his story is compelling, tragic, and quite honestly, Nirvana did impact music in a very dramatic way. Almost literally one day it was glam and arena rock, the next day flannel and "grunge".
Technically speaking, he was not a great guitarist. Honestly, he wasn't. The correct word to use is "limited", and I say that because he did the most with what he had - he wrote very intriguing songs with unique (especially for that time) lyrics and points of view. If he didn't know how to play the chord that word work, he made the chords he knew how to play work - and that is probably one of the coolest things about his songwriting.
Take the lyrics from any number of his songs and look at them without the music - they're poetry. You may or may not like the poetry, but it is poetry, without a doubt.
Now, as to whether or not songwriting should count towards being one of the greatest guitarists of all time, I dunno. That one guy from Dragonforce could literally play ten notes for every note that Kurt could play, artists like Buckethead and Satriani and Vai have done things that Kurt could never aspire to, Jeff Loomis and co from Nevermore could solo all over Nirvana, etc.
I think what Rolling Stone was looking at was more than just technical ability... but overall impact on music in general. There is no question in my mind that Slash has made an impact on music as a guitarist. Hell, he's practically the poster child for that bad-ace guitarist "look", and has written truly classic rock songs. And Eddie... it's hard to overstate the influence EVH had on music, when he came out with "Eruption" it literally changed the way guitarists nation-wide played the guitar.
Kurt made an impact on music. He may not be a great guitarist, but he was a very good songwriter, and he made an impact on music. I think that qualifies him for the top 100. Maybe not ahead of Slash, EVH, or many others, but I think it's a solid case for a guitarist of relatively limited talent to be included in a list of the top 100 greatest guitarists of all time.
However, if such a list doesn't have Django on it, it's a bunk list!