That's entirely what it is, and has no other bearing or qualifiers other than as a nod to the dominant religion of Western Europe when the written rules of the English language were set down.
Edited to add: As far as the society of the Imperium is concerned? No, it's definitely not secular, it's a theocratic dystopia. The High Lords of Terra, and all the Adepta and Ordos descending from them, as well as those who descend from the hand and word of the Emperor, rule in, and because of, his name. Now that he has become the God-Emperor, his authority (and thus the authority of those acting in his name) is seen as being divine in origin... and this is the lesson the Ecclesiarchy preaches from the pulpit on countless worlds of the Imperium. To disobey the word of the Administratum, the Arbites, the Inquisition, the Ecclesiarchy... is to disobey the word of the God-Emperor, Himself.
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