For those wanting to disable/remove Phone.apk, you can do so via adb shell/terminal.
I did so using this command after getting adb working
adb shell mount -o remount,rw /dev/block/mmcblk2p10 /system
adb shell mv /system/app/Phone.apk /system/app/Phone.OLD
due to different block/partition numbers.
Upon changing Phone.apk to Phone.OLD, there will be a force close notification.
Just "adb reboot" and your device should be fine on boot.
"mv /system/app/Phone.apk /system/app/Phone.OLD" will only rename the file.
You can remove it with a different command in shell.
Be careful with the command as you can delete all files within /system/app reversibly bricking your device.
Only use it if you understand how shell commands work.
If you are unsure, just leave it. Phone.apk only takes up 703kB. It is unlikely you will need to remove it for space, as we have Apps2SD (which is also the easiest way to install adb on your device)
You should be able to remove Phone.OLD using Root Explorer or other similar apps if necessary.
Please note that Settings>Mobile Networks will now force close due to phone.apk not being present.