Transceiver pulls both CAN wires to ground, when in standby. What does that mean for the other devices on the bus?
"Standby mode" is a specific active mode for the device, it assumes that the device will wakeup on any intended activity. If the device is not ready to wakeup it should be in "unpowered mode" (i.e., high impedance).

If the problem is that the micro controller is pulling the STANDBY pin up when it is not programmed, then add a pull-down to that pin on the MCP2542 to make sure that the CAN bus is either idle or in power-down mode.