It was totally fine. Borg implants or not, she was still human. She also didn't have a choice about becoming Borg at such a young age. When her connection was cut with the collective, she basically became a child again making her Janeway's responsibility. (That was close to Janeway's logic I believe, and I agree with it. It was a human decision for another human who was incapable of making decisions.)
The biggest thing is that Seven has already signed a contract with UPN, so she was kinda stuck for a few episodes anyway. Janeway knew this, so after thinking about it over a 50 gallon drum of coffee and a few packs of menthol Kools, she decided to just run with it and make it dramatic. (The Borg attorneys failed to overturn the terms of the contract even after several weeks of absolutely phenomenal work.)