Right, because in Narnia, you had things like Deep Magic from the Dawn of Time, and the Deeper Magic From Before the Dawn of Time, which got discussed in LWW. The Emperor put the magic into Narnia, although we never see him--- but we do see Aslan doing the work of Creation in TMN. So we think of the portals in Narnia as being magic because Lewis made it obvious magic was part of the world--- but it came from two different sources. Aslan's magic has nothing in common with the White Witch's magic, because one was healthy and sourced from the Emperor, and the other was unhealthy was based on witchcraft, even though both overrode natural laws.
re: the multiple deities, in Narnia, you had Tash and Aslan. But at the same time, Aslan wasn't an end to himself--- he was subservient to the Emperor-over-the-Seas, even though they were in perfect unity. The end of TLB has some good bits about how a person might say with his voice, or his thoughts, "I serve x," but by his actions, he actually serves y.
The Narnia books are also full of Roman gods and goddesses, especially in the earlier-written books--- Pomona, Bacchus, the river god, dryads, naiads, and so on. But they're basically created creatures who serve the Emperor in their own way as well, but with superpowers, rather than being a target of veneration in and of themselves.
So when I see a pantheon handled in fiction, I tend to be attracted to the type of worldbuilding that has multiple layers--- off in the background, you have your One Without Whom the World Cannot Exist-type God character, but those who actually interact with the characters are varying degrees of greater or lesser deity. They have a job to do, and they do it. In contrast with, say, the very binary good-and-evil fighting-for-souls sort of approach. I think the reason why that works for me, as a reader, is that I'm more inclined to contrast my personal RL ideas about theology against the binary version, whereas I'm more inclined to treat the layered pantheon approach as ordinary worldbuilding. CS Lewis did it well--- Bujold also did an excellent job with her World of the Five Gods series.
As a Christian writer, I think the key is whether the superpowered stuff happens With Divine Approval, or Apart From Divine Approval But He Allows It to Happen Anyways Because Free Will But It Will Eventually Catch Up To You In a Bad Way Because That's Why It Wasn't Allowed In the First Place Because It Harms You And Others Whether You Know It Or Not. Stuff that happens With is going to be good, whatever you choose to call it; stuff that happens Apart is going to be bad, whatever you choose to call it. But that goes back to the nature of your power's source.