What reason would he have to lie to us? It makes absolutely no sence that he would do that.
Seriously people your reaching for stuff because you just dont like the game. I can see of no reason why it would have been a lie. In fact it seems like the truth because of the wording in that film.
Gold Elite: "What if the infection defiles the relic?"
Arbiter: "I care not for your little life. Open the relic"
With these two lines, yes they are direct quotes with exact wording, it seems to lead that the "infection" would have come from outside the structure not inside. If the Flood were inside the structure already would you not think that the relic would have already been defiled? Seriously read these lines and watch the video again. Your reaching for nothing but air.

Approval of situation A recognized. Commensing the Cromwell Invocation. Ability restrictions lifted for limited use until the enemy has been rendered silent.