It can be explained by what perspective you examine the dark-grey-light issue from. Almost all the dialoge options reflect something that is unique to one of the three alignments. Some of them display greed, selfishness, arrogance etc., which are the signature signs of the dark side. Some of them exhibit self-sacrifice, care for others, selflessness etc., which are light side qualities. If you are more into Star Wars, then you know that if you keep expressing the thoughts of either of the two types of qualites or keep acting in either of these ways while being force sensitive, you will finally be committed to either the dark side or the light side, depending on which way you've chosen. It is the perspective of the force.
If we examine it as outsiders, not being force sensitives, the things written above don't apply. Being 'outsiders', we think that what Kreia represents can't be considered to be evil or good, because she, basically, doesn't adhere to either of the two extremes, she's just rational. On the other hand, what she exhibits are self-reliance, self-sufficiency, distrust, selfishness etc., which ultimately make her a dark side person (of course, from the force perspective).