Hi, I attended Penn so I know the area. She's smart by staying out of West Philly, which is where Penn is located. It wasn't that great many years ago and with crime skyrocketing due to lax enforcement it's not getting any better. Even parts of Philadelphia that were considered relatively 'safe' are seeing regular violent events nowadays.
Your daughter is smart to be thinking about places that can access Penn without driving, especially as traffic is very bad (and parking almost impossible to find in some areas). Traffic will just get worse as office workers return to the office. Further, there has been an uptick in carjackings and catalytic converter thefts so driving is no longer completely safe either.
There have been increasing acts of violence on the public transit systems, mostly the subways but I would also avoid the bus systems. If she wants to take public transit to work I would recommend (in the name of safety) to ONLY look at the SEPTA regional rail lines (or if she has a lot of money, Amtrak). Basically you want a line that doesn't go through any of the bad areas of Philadelphia, to avoid picking up any bad actors.
In particular, given where she is looking, the Norristown high-speed line (the so-called "flying coffin") is off the table, because it starts in a not-so nice area (Upper Darby) and ends in a similarly sketchy place (Norristown -- with all apologies to Bill Geissele). Worse it connects directly to the blue line subway (Market-Frankford) -- which might be tempting as it goes directly through Penn's campus but it goes through the area of Philly that is known for drug tourism (Kensington) and you will find a lot of tweakers riding that line.
Without knowing more about your daughter's preferences I would say look at where the SEPTA R5 Regional Rail line (aka Paoli Thorndale) runs (west of Philadelphia). It runs mostly through wealthy western suburbs and drops her off nearest to Penn at 30th Street Station, which admittedly is 3-4 blocks from the east edge of Penn's campus. This line has the disadvantage of not stopping at the Penn Medicine regional rail stop, which may be closer to her work location. If she is looking at the Main Line (a safe suburb) then this is right up her alley.
Manayunk should be relatively ok and I would not have an issue with her taking the Norristown Manayunk regional rail line (note this is not the same as the flying coffin line, which is the Norristown high speed line) although it does stop at one or two stations in sketchy areas before getting to 30th Street Station (Temple University, North Broad Street and Allegheny stops). The Norristown Manayunk regional rail line stops at 30th Street Station and at Penn Medicine.
Hope it all works out!