I doubt the filings do anything to the turbo as they'll be blown through the housing upon initial startup, not like there's any serious exhaust gas velocity at that point to cause the filings to hurt the wheel.
I was told by a friend to drill mine out with the motor running. This would blow any chips out towards me instead of through the turbo. Also, start with a small bit and work your way up to the size you need. This too will help make the chips very very small.