Just he said, he said until one of the parties actually releases documentation (Wired can release emails showing Kapersky's co. cooperated closely with the fact checking, Kapersky can release docs to show the opposite, etc.)
As someone who is a casual reader of Wired and knows little about Kapersky, I don't know who to believe. Russian stereotypes and the current actions of Putin's government would push me towards believing the Wired article but that doesn't make me comfortable enough to say anything with confidence.