Let me think... I don't believe I have, but only because I haven't had a reason to currently. Most magic-users I've written recently aren't wizards or witches. They could be considered as such, I suppose, but they're not.
I would most certainly write such a character if I ever had a reason to! I--oh, wait, I think I did write one once. Several, actually. Only I called them (and their apprentices) sorcerers. I just liked the sound of it better than 'wizards'. This was a few years back; I'd just watched Nicolas Cage's version of "The Sorcerer's Apprentice" and had fallen in love with it. Hence it inspired me.

I don't think it's wrong to write or read wizards and witches at all. It's not like we're practicing witchcraft or actually believing the stuff, so what's the fuss? If we didn't write/read what the Bible said was wrong... well, there wouldn't be any stealing, killing, lying, cheating, gluttony, greed, envy, etc. in our stories, and we would hardly be able to read anything anyone else writes! The list goes on and on. Why should witches and wizards be any different? And why shouldn't we break the mold of 'bad witches and bad wizards' and make them protagonists? Or at least good characters rather than villains?
After all, as you said, Tolkien did a wonderful job with Gandalf (whether he was an actual wizard or not)!