Well nobody reported deleted files or whatsoever with using pyfragtools, so I guess it's ok

I'd use it on a PC tho, with ubuntu for example, since it's said to use quite a lot of ram memory
Well reading is easier, since you know where the file fragments are at.
Writing requires the drive to look for an empty place, so that usually causes some slowdown. yet... 50KB/s is really slow, so I doubt if it's all to blame to the fragmentation.
Have you checked bad blocks already? this takes quite some time btw.