Why did this brown rice recipe fail?
This recipe should definitely work if you follow it correctly. Comparing your recipe to it might tell you what you did wrong. From the information you already gave, it seems certain that you didn't cook it long enough (as rumtscho said in the comments). Other things that could have been wrong:


oven not hot enough (your oven might not be as hot as you think)
water not hot enough when added to the rice (Alton Brown's recipe calls for it to be boiling; I don't know about yours)
too much water/too little rice
dish too small (if the water is deep, it won't heat as fast in the oven)
(thanks to Aaronnut, see the comments) non-metal casserole dishes take a while to heat up


Given your updates, well, basically I have no idea how that recipe would ever have worked. As you saw, the water wasn't even hot enough yet after half an hour. If you poured the water in boiling, it might have had a fighting chance, but it still would probably not have been long enough.

Cooking it uncovered is weird, too - it means that once it's hot, you'll start losing a lot of water to evaporation. The recipe on the bag likely has you cook it covered on the stove, so clearly you shouldn't be using the same amount of water with it uncovered.

As for the amount of water... 1:2.5 really sounds like too much water to me. I've seen some people online claiming that 1:2 is right for white rice, and brown rice needs more water, but in my experience that's a recipe for soggy, watery rice. (Edit: Of course I was basing that on covered rice; rumtscho rightly points out in the comments that for uncovered rice you'd need even more, since you lose some as I mentioned.)

So if I were you, I'd forget about the recipe you used, and try the one I linked to. Many people (including me) have had reliable success with it.