Everything with Apple is proprietary and people come into the ecosystem knowing this. Besides at that time Skype could be used as an alternative.
There’s the rub. Apple’s ecosystem is proprietary. Some features/abilities, it limits to its own apps. Those abilities are often highlighted in their marketing.
Facetime was so integral to Apple’s early iPhone marketing boasts, that not only was it preinstalled, it couldn’t be deleted. That implies that the service was inseparable from the hardware.
Judging from Apple’s eventual concession to allow users to omit or delete many of Apple’s stock apps, Apple is probably avoiding future lawsuits like this one.