They did think through it, but the rover has already exceeded its planned mission time by over 2.5 years! Wheels can't last indefinitely, and more than doubling the time of a 2 year mission before they see any wear is pretty incredible.
The tires are exactly as strong as needed to perform the primary mission, and no stronger. They are doing that easily. This was successful engineering, not some mistake.
There are a combination of factors not mentioned in the article:
One, encountering terrain with unexpectedly sharp, immovable rocks.
Two, a suspension arm design that happens to put increased force on certain wheels when they encounter immovable rocks.
Three, the wheels have a tread pattern with a sharp, angular geometry, causing stress risers at the points of the pattern, where the thin metal meets the thicker raised treads. The thinner metal thus tends to crack more readily at these points.
(BTW, it is only this last point that I consider to be a legitimate design flaw, given the innumerable constraints the engineers had to work within. The rover is a marvel of engineering on every level.)
In all seriousness its unclear to me how this could happen so quickly? The article does not really explain why they didn't think through this.