My thermometer probe is poking holes in my BIAB grain bag, what do I do?

The diameter of the thermometer's probe is roughly 6.5 mm, which closely translates to 1/4".  

Use a small snippet of 1/4" ID thin walled (5/16" OD) silicone tubing and slide it over the probe. 

That should buffer the thermoprobe's point against your grain bag but also not inhibit its ability to display an accurate temp.