If she was, the Lady of Pain is not listed as a major inspiration though it's not impossible that she could have been. Pharasma was one of the deities imported from James Jacobs' homebrew and he lists his inspirations as
-Neil Gaiman's Death from Sandman Comics
-Wee Jas (old 3.5e neutral death/magic goddess) from Greyhawk
-Osiris
-Charon
-A bit of Kali
Now, presumably at this point in time over a dozen people have written for Pharasma, so it's possible she's grown beyond these origins, or it's possible that others have drawn a connection to the Lady of Pain and created more of a connection in theme. Possibly even James will come by himself and pull the curtain back a bit. I especially enjoy learning about deity origins and inspirations behind old lore elements, so one can only hope.