Yeah, that Vex stuff is almost directly lifted from a thought experiment from a rather loopy group of amateur philosophers who are particularly obsessed with AI. Google "Roko's Basilisk" for some reading material. It's hard not to feel as though this is just the latest from a voice that has always been around at Bungie.
It's all about recurring motifs - dreams within dreams, deities painting new worlds from the colors of their experiences. When Rasputin shows up on Mars, Ghost comments that "he's everywhere now" - no doubt in my mind this signals an upcoming story arc in which he proves just as unkillable as his namesake. Doesn't that sound like Leela's fate, inextricable from a multi-planetary network? Even the traveler's story has shades of Durandal's return to Earth.
There's no sign of a Charlemagne or a Joyeuse yet, but Destiny's story at the moment is little more than a whole lot of stage-setting. There's plenty of time for those names to turn up.