nrf_rtc_timer: clear events and counter when disabling sys_clock

Clear pending IRQ when starting and restore back the RTC1 state when
disabling sys_clock, to avoid issues when soft rebooting the device or
chainloading another Zephyr image (e.g. mcuboot).

Change-Id: I693d9168196ad2cfb8475ecfa2051eac043b1fbd
Signed-off-by: Ricardo Salveti <ricardo.salveti@linaro.org>
(cherry picked from commit 6713088cfc813f14e442e4acc01c4c85959dd8df)