Standards are not a reason to design insecure systems. While Apple has no control over the standard, they do have control over their systems.
Apple already gives security alerts when SSL-CERTS do not match the domain used. There's no reason why Apple could not give an alert if the display and response number for a SMS differ.
Further, their response that iMessage fixes this issue appears to show they knew of the issue, but decided not to design a solution for the iPhone's SMS system without breaking the SMS standards; which is possible, see the example below.
Here's an example of what an alert might look like that does not break the SMS standard, but warns the user via a security alert message:
