Freezer bags are supposed to be microwave safe. If they are microwave safe, it seems fine to put boiling water in them and let sit. That being said, I don't use freezer bags for cooking since I haven't ever had trouble cleaning out my Jetboil, at least sufficient for my standards on the trail - meaning I don't worry about getting it perfectly clean. Reason being that when I boil water the next morning for breakfast, I let it boil a bit longer which in theory should sanitize the pot before I eat from it again.