I'm certain there are, which is why I have speculated before at the prospect of Human, Awoken, and Exo enemy NPC. The idea of rogue guardians have interested me ever since I started researching the Destiny lore in depth and it makes reasonable sense. After all, the Traveler has many enemies, and the idea of a civil war is not unrealistic.
However, I'd also rather see this conflict show up later along the Destiny storyline. The concept of infighting seems a bit axillary in concerns to the early missions of the game, and I think we need to focus on building the foundation of the enemies we already have. The way I imagine rogue guardians being introduced in the story wide-scale is via an event arc somewhere after we've exhausted the introductory courses of the 4/5 enemy races; perhaps even allowing players to temporarily side with the insurgents.
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Agree, insurgent conflict should be present in future expansions. I really like to read well written ideas. good job.