Not that I'm aware of, most still use pedalboards - and I don't blame them really. I use a pedalboard at the church I play at because it's way easier for that application (in my opinion) and makes transit a breeze. I could bring a guitar, the AxeFX II, a MIDI footswitch, more cables and an extension chord/power bar... or I could bring my guitar and pedalboard and go straight through a DI and it sounds excellent. Plus I think you'd be hard pressed to find any Christian musician wanting to spend that kind of money on the unit, knowing how hard it is to make any money doing so.
I also think it's a practicality thing... with worship music there's a large amount of it that is improvised, in a way. You need to pay attention to the congregation and work based on their reactions. If you've got everything pre-programmed in your AxeFX II for your set list and one thing changes, you could be in quite an unfortunate situation. Maybe they just aren't feeling that new song you want to try, so you make a last minute decision to play it half time and more chill, to allow people to enter into worship more. But the patch you had in mind has lots of overdrive and a really prominent delay! With the AxeFX II you'd have to go back over to the unit and tweak all your settings, or find a patch that fits what you want... if you're lucky enough to have made the one you want already. With a pedalboard you turn the gain down on your overdrive, and the mix down on your delay and you're good to go!
Another scenario would be if you've played a lot of slow songs back to back and you can feel people getting bored - you decide to keep with the set list as planned, but bump up the next song and create some motion. So instead of that ambient pad sound you had in mind, you go with a straight overdrive sound with a bit of reverb and decide to do some steady 8ths to keep the movement in the song, and keep it pushing forward. Again, maybe you have an AxeFX patch for this already, maybe you don't. With a pedalboard it's all right there and takes much less time to make these quick decisions on the fly, or even just experiment with sounds if you want to. It's all RIGHT THERE. This makes it easy if you're not the one leading either, and the worship leader notices the crowd and tells you "Do some pads in the bridge!" 8 bars before the bridge.
That being said I would still recommend using it for worship music, it would certainly get the job done and sound awesome using it. Just because no one else is doing it, doesn't mean you shouldn't. Nothing wrong with being different, in fact I would encourage it! I just wanted to point out why some people (myself included) would not see it as the ideal system for what is required.