I think that with Mariner, the point is that despite SF protocol, she may think its the best way to leave her mark on the galaxy and help others, plus she went through the academy on top of everything else.
Its also possible she wants to institute her own reforms in Starfleet which would get rid of needless bureacruacy that slows things down, and also to check up more frequently on societies and civilizations they encountered to see if they followed through after being helped initially - she may not have necessarily made this realization though and thus keeps her rank of ensign.