In effect her question was this: What if your story really is about forbidden love, or about choosing between life and love, or could be quickly described by some other cliché? Are they saying you can't query it?
Of course you can query it. If there are only four (or eight or twelve) standard plots in the world, you can assume there's going to be some repetition.
Therefore it's up to you to do your future literary agent a favor. Assume your future agent goes to her inbox every day to find a hundred new queries. She's read all the clichés. She wants to find something she'll enjoy, but in order to enjoy your story, she needs something to remember. Something specific.
Remember that a cliché is a shortcut. And when you use one to describe your own work, you're giving only a surface rendering of a story with depth. Work harder. Give it that depth.
Read more (courtesy Query Tracker)