There's a way, but it's a bit complicated.
The software reset happens because the reset line of the ATmega is connected to the DTR line of the serial connection (coming from the FTDI chip) via a capacitor. Whenever the DTR line drops, the chip resets. The FTDI drivers lower the DTR line whenever you open the connection. If, however, you set HUPCL when the connection is open, the line will not be raised when the connection is closed. Thus, the next time you open the connection, the line will already be low, so it won't fall and reset the chip. You can set HUPCL from C, but I don't have the syntax handy.