The partition part is about how tolerant your system is to a partition situation. Having massively reliable communications between systems will reduce your MTBF, but it doesn't address how your system will actually handle a partition. You do need to account for it one way or the other. If you get a partition, you can't keep operating with consistency across the whole system.

Now when you look at patient data .. sure, eventually consistent might be just fine.. but that's not consistency as referred to in CAP. So while it's perfectly acceptable to your app, it's not about making CAP invalid.