commander: ignore arm/disarm in DO_SET_MODE cmd

According to https://github.com/mavlink/mavlink/pull/629 the mavlink
command DO_SET_MODE should only determine the mode but not the
armed/disarmed state, so the MAV_MODE_FLAG_SAFETY_ARMED bit should be
ignored.
Instead the mavlink command COMPONENT_ARM_DISARM should be used instead.

Therefore, the commander now ignores the arm/disarm bit.