Another good way to avoid substrate ingestion is to use a separate container specifically for feeding. I have rept-carpet and I still do this simply to keep my snake from associating her tank opening with feeding time. It's kinda cool to watch actually how she will go from very docile and mellow to full on hunt mode as soon as I put her in the feed box.
Also, great suggestion on the tongs. My snake refuses to eat unless it's moving and it only took me getting bit once while wiggling the mouse with my fingers to realize that was a pretty stupid idea.