The vex aren't only at war with humanity. Really if they wanted to they could just go back in time and turn earth into a machine world, ending humanity before they began. They see a use for humanity and the traveller and wish to understand "the light" rather than destroy it as it has a use to them. Hence they convince you to rid the vault of glass of the taken energy by letting Praedyths messages through because they were unable to fight it themselves.