You seriously expect Xur to take sides? Or understand the concept of sides? Xur is the most freaking mysterious character in the entire game, maybe even more mysterious than the Exo stranger. Also, if bungie doesn't want to have an official lore explanation for the six person raid limit, I'll put one here:
Some people think that the more light you have, the easier it is to drive out the darkness. It is not so. The greatest scholars of the Golden Age knew that the closer you get to the light, the larger your shadow grows. When extreme volumes of light and darkness meet, unpredictable reactions happen. Sometimes, one side is completely destroyed. Other times, time and space itself may be rent asunder. It is theorized by some that the Vault of Glass does not actually exist unless guardians with strong enough light come to challenge it. At that point, their light reacts with the darkness, as Sodium would with water. This reaction skews the normally linear course of time, and allows the Vault of Glass to open. Note that I myself do not agree with this theory, but some 'free thinkers' *cough* Lakshmi-2 *cough* firmly stand by this theory. If we sent the entire army of the Vanguard down to the dark below to face Crota, the risk would be too great. There would be a chance that the army of the Light would be destroyed completely. We could not take that chance. We could not afford to have a repeat of what happened the first time we tried to reclaim the moon. The guardians we sent down were mainly a scouting party, to ascertain Crota's location and power. The knew the risks, and went willingly. With one of the party now back, we hope to end the threat of Crota once and for all.
-Ikora Ray, when questioned by a young Guardian why the Vanguard did not send an army to destroy Crota
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Give this man a job at Bungie asap!!!