arduino mega got 12v in 5v output pin

The power from the USB goes directly to the +5 volts on the board, so you will always be able to power the board even if communications isn't working.

It's up to you of course, Hugo. If you buy or build a programmer that will work with the six pin connector you will probably have a usable board. I have an Arduino serial that I bought a board for and I didn't even hook up the serial port. Adafruit has the programmer built right into a USB cable for $20. There are inexpensive kits and plans all over the net. So if you ever feel like using it, that's how to do it.