The problem wasn't so much that she resurrected him, as how she did it. She controlled time itself and wrapped it around him, giving him life with a power that she didn't understand. Imagine it as someone who has a prosthetic limb and needs to learn to control it. She tried to place something (his life) gently back into time and instead punched out violently. Time around him solidified as if it were that paste that goes solid with kinetic energy.
She made it so that his death was something that just couldn't happen, wrapping him in time energy that jumpstarts his system whenever he dies, almost like an antivirus seeking out a problem with a program and fixing it. Of course, over time that energy would wear down and eventually dissipate, in this case by his own choice which allowed him to finally die. Exposure to time travellers would likely drain some of the energy too, as would the vortex he guarded in Torchwood.
It never got explained but I like to think that the whole Face of Boe thing came about due to cellular mutations introduced in his system over the course of millions of reconstitutions over the years. Having the effect turn off (like it did in Miracle Day, for example) every so often would allow him to be mutated from radiation enough that over centuries he could become as he was when he died. That's my personal view on things.