It's been a few years since I've seen the ending, but I was under the impression she wanted Magus to finally be free of the pain she had caused him. After all, he had devoted his entire life to find and free her, and ultimately it was all for naught; it was a task too large for him to complete.
Perhaps, from her glimpse of the timeline(s) in the DBT, she was fully aware that only Serge could save her with the Chrono Cross element. As such, she knew the futility of Magus' mission, so she urged him to seek freedom. Knowing that he was too stubborn (and zealous) to simply abandon his search, his only option would be for him to forget about her entirely.
That's the way I look at it.