Happened at my church as well. Was working fine for a practice & a service, then halfway through the next practice, the sound guy turned on phantom power while troubleshooting some piano mic noise, and it was awful. At the time, I unplugged the Helix and went back to a real amp.
I haven't played again with the Helix at church because I've been mainly playing bass lately, but when I go back to guitar I'll definitely insist on them turning off phantom power on my inputs. It was dead silent before that.
...and I'll still carry around a DI in my Helix bag just in case... but really there's no excuse to NEED to have phantom power on in any modern console.