I lived in Philly from 2000-2003 and am still a regular visitor, and I never felt unsafe while running there. I ran in pretty much every area except right around Temple, so I cannot comment on Temple per se. But West Philly and South Philly are perfectly fine, probably affordable, and with easy access to the river and Fairmount Park, where most of the best running is. I lived in West Philly myself. If I moved back, I'd also look seriously at Roxborough/Manayunk.
(Actually, I take my comment about never feeling unsafe back: the one time I was worried about safety was when I ran across the bridge to Camden to visit Walt Whitman's grave; that area was so unpleasant that I turned around before getting to the gravesite. Also, there _are_ small stretches of West Philly that I would avoid running through)
On the issue of your graduate experience, one thing to consider is that there is a much larger academic community in Philadelphia, with Penn, but also Swarthmore, St. Joe's, Villanova, Swarthmore, etc., etc., in close proximity. This can make a real difference in terms of visiting speakers you can get to interact with, other people specializing in your field you'll be able to look up easily, etc.