I think you're mistaken. This was in the middle of the article....
"The new engine has a cast-iron block, like the current 4.7, and both use 32-valve aluminum heads. (The 5.7 block is aluminum, to reduce weight, which also adds expense.)"
Again, based on the information I've read, the new 4.6L is more similar to the older 4.7L than it is dissimilar.
I hear what you're saying regarding aluminum blocks, but engineering capabilities and manufacturing techniques have come a long way in just the last decade or so. Historically, the biggest issues with aluminum blocks has not always been the blocks themselves, but how they interact with dissimilar metals (i.e. aluminum block and steel heads, or vice versa, expanding and contracting at different rates, etc.). While you can easily make a case for a cast iron block over an aluminum block, I think we'll see more and more engines coming with aluminum blocks in the future.
With all that said, I wouldn't hesitate to drive a truck with an aluminum block. There are many here that have 200k miles on their 4th gen V6's with no major issues to report. I think engine longevity has more to do with driving style and maintenance then it does engine block material. But that's my perosnal opinion.
And not to veer completely off topic, but I've also found that most cars and trucks, regardless of make, model, etc. experience far more costly repair issues with components other than the engine far sooner than before you have major engine issues. I owned two Jeep Grand Cherokees, one with the 4.0L straight 6 and the other with the 4.7L V8, and I got rid of them long before either of them had engine issues due to tranny issues, brake issues, electrical issues, etc. So regarding the 4Runner, I would have no problem owning one with an aluminum block or a cast iron block. I think both are solid engines.