I'm of the opinion that not everyone in the Covenant was a blind zealot. I think, as with any faith, there are those who take said faith a little further than others. There are of course people who believe unconditionally (Xatan'ee, Pel and others) and there are those who believe in the Journey but do not froth at the mouth over it. I don't think the Covenant hierocracy would kill thousands of soldiers purely because they surrendered in the face of overwhelming odds. Is that not how the Covenant was formed? Through the battering of races until they eventually gave up and joined the Covenant? Now, I don't completely adhere to canon with this story, maybe. Because if the Covenant was a completely alien culture to ours, there would be no relation to the characters and events. I like the idea of the Covenant being trapped in faith, but not completely besotted by it. There are radicals as with any religion, but most Covenant in my eye are just normal practitioners of the faith. These Covenant tend not to be in the higher echelons of rank, though, and we are very rarely shown the 'common' side of the Covenant in official Halo media so I think I can take some creative liberties.