We use CLE for all of our Amtrak trips (just returned this morning at 2am
),
The area around the station is pretty isolated from the downtown so you do not have street people, etc/ roaming around the station. The gated parking lot is pretty safe. We have left our cars there on all trips without incidents. There are always two agents on duty.
There are always cabs waiting at the station when trains arrive. The station stays open until 1pm so no problem waiting in the lobby for her ride to pick her up.
You noted she would arrive around 6am so I assume she is taking the Lake Shore instead of the Cap Ltd.
I would not be concerned about her at the CLE station.