Board Thread:The Flash discussions/@comment-11526603-20160401014522/@comment-3423279-20160401015858

Umm.. those events hadn't yet occurred, and Eobard Thawne not returning to his time so as to eventually kill and replace Harrison Wells, create S.T.A.R labs, and become the mentor of Team Flash is what was killing Cisco as that timeline was being erased.

McGee wasn't really a factor in that.