By the time you boil the water in your pot, turn off the stove, remove the pot from the stove and then pour the water into the freezer bag, the water temperature will be low enough that you won't have exceeded the recommended temperature for the freezer bag. This is certainly true at higher altitudes. Remember that freezer bags do not contain bisphenol-A, the chemical causing the current controversy.

If you're really concerned about freezer bags, then you can get one of those sealing gizmos with the kind of plastic used for "boil in bag" meals. The only thing is that unlike a ziplock bag, these bags can't be resealed once opened. Not a big deal if you keep them upright in a stiff cozy.

I would bet that your Mountain House foil bag has a plastic liner, anyway. And if that liner is the same material that is used to line canned food containers, it does contain BPA. I'd be more suspicious of that than of a freezer bag.