I have found a workaround for kernel 2.6.30 here:
http://www.at91.com/forum/viewtopic.php/f,12/t,12783/to change USART in RS-485 mode, add this line in linux/drivers/serial/atmel_serial.c , in function atmel_set_termios ,
just before the instruction "UART_PUT_MR(port, mode);" that configures the USART mode.
if (port->irq == AT91SAM9260_ID_US3) // USART3 is a rs485
{
mode |= ATMEL_US_USMODE_RS485;
}