If it had probably been brought up back home, Elena probably would have factored Stefan into her answer. She did love him, but being away from him made her feelings for Katherine show more. And while she wasn't sure if it was love yet, it wasn't the same as Stefan. It was hard to explain, but Katherine was the one she wanted to be with.
When Katherine's lips pressed to Elena's, she kissed her back before Katherine pulled away. The mention of telling Stefan made Elena's look away, however. It wasn't that she was unsure of her decision, but telling Stefan that she was with Katherine would be difficult for many reasons. "That won't be easy to do," she pointed out. The main thing being the hatred Stefan and Damon had for Katherine. She had hurt them and she was sure that they would hold it against Elena if they knew. Then there were the things that no one would accept. Like the fact that they were family--even if distantly removed--and they looked like twins.