While Apple hasn't expressly condemned modding the iPhone or put up a legal fight against people doing such, they still are keeping their word regarding servicing phones that show signs of modification. Their disclaimer for the phone includes the ability to deny you warranty service if your phone was modified, and they are doing just that.
While it is easy to get upset by this - after all, a software mod shouldn't void a hardware warranty - that's still Apple's policy and anyone who does tinker with their phone is likely aware of the risk. The blog mentions a very good point that anyone fiddling with the inner workings of their iPhone would do well to remember: reset to defaults if you need to send it back:
So while he eventually got Apple to return the iPhone (after paying the restocking fee, that is), the lesson here is to do a restore of your iPhone and re-install the factory AT&T SIM before bringing into an Apple Store for service. That's the beauty of software-only hacks, after all!
Truly, you cannot criticize Apple for taking this stance. They sell the iPhone as a hardware and software bundle, and don't intend for it to be taken apart. With modding there is always a risk for the manufacturer to give you the cold shoulder when it comes to an RMA.