I am guessing Clarke uses the term Pure Intellect as a name for a certain entity, possibly of strong AI, an all encompassing intelligence. We cannot begin to imagine what such an entity would think of, or do. Clarke himself is quoted as saying: Any sufficiently advanced technology is indistinguishable from magic.
Ray Kurzweil, an inventor and expert in cutting edge technological trends, proposes that such an entity is not only possible, but inevitable.
About your question, the comparison to God is unavoidable when one speaks of all powerful entities. We can't help it. Clarke, much like yourself, knew what his term "sounds" like. Many science fiction writers use this effect in their stories. Read Assimov's "The Last Question" for the best last line in science fiction history, and as an added example of my point.
