safe i.Mx6 GPIO out -> REQ. arduino all pins INPUT???

An Arduino Pin on Output, stays on Output after Power Off/On. Right?

So if I have a blinking output Pin 13 on Arduino (Sam3x), I can destroy it, by also doing GPIO ouput from i.mx6.
Correct?

Example:
How to destroy pin 13:
Arduino (Sam3x): blink on pin 13

Code:

int led13=13;

void setup() {
    pinMode(led13, OUTPUT);
}

int state = 0;
void loop() {
    state = !state; // toggle state
    digitalWrite(led13, state);
    delay(1000);
}

i.Mx6 (toggle same pin, but different delay...)

Code:

## in a shell
echo out > /sys/class/gpio/gpio40/direction
while true; do
    echo 1 > /sys/class/gpio/gpio40/value
    sleep 3
    echo 0 > /sys/class/gpio/gpio40/value
    sleep 3
done

Is it true that this will severely mess up and destroy pin 13?

So my actual question:
If I really want to do GPIO from i.mx6, I have to load a "dummy" arduino sketch that ensures all pins on Input. Correct???
Is there not a better way? Or any other way?

"dummy" arduino sketch that ensures all pins Input.

Code:

void setup() {
    int i;
    for (i=0; i < 54; i++) {
        pinMode(i, INPUT);
    }
}

void loop() {
    delay(1000);
}

Will this work?

Thanks for pointers and insight.
P.

 

If you cut the power the Sam side should go back to default .
I`m 99.9% sure this is what happens !!!!

1/ You power cycle !!!! .... REMOVE THE POWER .... and power again
2/ The Sam runs the boot loader which set all gpios to their default state.
3/ The Sam now runs the script which sets the pins via pinMode(led13, OUTPUT); etc

I can`t see why not