pwm: atmel: Fix polarity handling

When atmel_pwm_config() calculates and then sets the prescaler, it is
overwriting the channel's CMR register so we are losing the CPOL
configuration.

As atmel_pwm_config() is always called before enabling a channel,
inverting the polarity doesn't work.

Fix that by reading CMR first and only overwriting the prescaler bits.

Signed-off-by: Alexandre Belloni <alexandre.belloni@free-electrons.com>
Acked-by: Nicolas Ferre <nicolas.ferre@atmel.com>
Signed-off-by: Thierry Reding <thierry.reding@gmail.com>