Is that from a text? Because that sentence is phrased in a very strange way... It makes sense, after reading it a couple times, but it's very strange o_o .
Anyway, the phrase in question simply means "in favour of a deity".
Quote:
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and therefore so far as it goes it affords a moral argument against deity and not in favor of one
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"So you can reason that as far as this is concerned, there is a moral argument AGAINST a deity rather than in FAVOUR of a deity."
Hope I'm not too late to be of help!!!