The Ethernet PHY configuration is a one-time event. Once the configuration has been completed using MDIO and MCLK, these pins will no longer be required. It will then be possible to switch the pin function to USB.
Another option is to use Ethernet MII Management (MDIO) using software. This is described in Application note AN10859.
If MDIO is implemented in software, there will be no need to share pins between USB and Ethernet.