Unfortunately, I think it resonates pretty well with certain modern people - the types who look at any reference to magic or witchcraft as being contrary to god. For them, it seems there is a divide between divinely sourced miracles and other forms of magic - and that the latter is inherently tainted because it isn't of god and thus must be against god. I won't veer any further into religion and politics other than to bring that up.
I understand some concern that even that divide offers no particular reason that the two magical sources can't duplicate certain subsets of each other's effects. But, ultimately, with many different influences to draw from - none of which are definitive within mythology or fantasy literature - D&D was free to arbitrarily set up its own structure. That's a great cover for building class niche protection into metagame structures without it requiring too much metagaming at the in-game player level.
Thats all true, but i still dont like it. IMO the Palidan should be the cleric, mages should be the priests and "clerics" should be a job title, not a PC class.
I know it will never happen, but i can always hope.