That command will completely disable Ethernet PHY, isn't it? It is the way, but I already use EPHY in my design, so no.
No, the ephy label in omega2-ctrl is misleading, it does not control ethernet phys, just the LED.
See AGPIO_CFG register for enabling/disabling ephys 1..4 (all together either ephy or GPIO, unfortunatly it is not possible to selectively enable only one of them -. ephy0 however can be used separately, with ephy1..4 in GPIO mode).
When I was designing a PCB for Omega 2S, I haven't had all the docs, and as a result I've used some of I2S pins, almost all SPI pins, etc. (literally, all the pins that could cause boot and other problems when they are pulled up/down) as a GPIO.
I was in the same situation a while ago when trying to find a usable wiring of my first Omega2 and Omega2S circuits, with all those various constraints...
To see all options for all pins of Omega2 and Omega2S at a glance, I augmented the official pinouts a bit in a PDF, including boldface labels matching the pin names in the datasheet and red labels on the pins that must not be pulled up or down at boot. That started in a forum thread about this back in the first Omega2 days...
Still, this is my most often used PDF when designing new Omega2(S) PCBs, maybe it's of use for you, too.