How to achieve an interrupt frequency of 100 kHz on SAM E70?
Thanks to @Justme, I've managed to configure the interrupt for 100 kHz. The problem was that the timer wasn't set to a width of 32 bits and the function tc_find_mck_divisor doesn't 'know' that. The following code is a solution  that still works with a 16-b timer register (provided the master clock runs at 150 MHz):

int main (void) {

    sysclk_init();
    board_init();

    pmc_enable_periph_clk(ID_PIOC);
    pmc_enable_periph_clk(ID_PIOD);

    // Turn onboard LED off
    pio_set_output(PIOC, PIO_PC8, HIGH, DISABLE, DISABLE);

    // Timer and interrupt configuration for 100 kHz interrupt frequency
    pmc_enable_periph_clk(ID_TC0);
    tc_init(TC0, 0, 1 | TC_CMR_CPCTRG); // set prescaler to 8 (TCCLKS = 1)
    tc_write_rc(TC0, 0, 187);   // 150 MHz (MCK) divided by 8 (prescaler) divided by 100 kHz - 1.
    NVIC_EnableIRQ((IRQn_Type) ID_TC0);
    tc_enable_interrupt(TC0, 0, TC_IER_CPCS);
    tc_start(TC0, 0);

    // Turn onboard LED on
    pio_set_output(PIOC, PIO_PC8, LOW, DISABLE, DISABLE);

    while(true){};
}