I can see how she can be a bit of a cliche, but there are people who feel that way. I was surprised and relieved that she didn't become a romantic interest for Kirk. I liked that he was relating to her strictly as a professional, and not trying to put the moves on her too much.
I was disappointed with how little regard, or even any discussion, was made over the effect to the timeline that removing Gillian from the 20th century would have. After all, that was the main plot point of "Tomorrow Is Yesterday" with Captain Christopher.
I'd think I'd say that she wasn't strictly a romantic interest for Kirk...but there was a definite vibe there. I don't think Kirk went on a pizza date with Gillian only to get information on the whales from her. There is also an implied flirtatious future possibility in her line, "See you around the galaxy" when she hugs him at the end. That's my take on it, anyway.
But your point is well taken, whatever romance element that's there is secondary, and her character is integral to the story; she's not just another "babe of the week" for Kirk to bed.