I'd go with a combination of suggestions here.
1) Tape over the mobo around the affected area, cover a good section.
2) Use double sided tape - any filings that land on it will just stay put :-)
3) Cut a new head into the screw - less metal shavings than drilling it into oblivion.
4) Use a vacuum cleaner nozzle right where you are cutting
5) Give the whole thing a damn good clean afterwards
That should minimize risk of rogue filings shorting something later.
