The question that we can't answer is that if Quaid wakes up in Rekall, how is it done? You have to assume that there are programs to ease him back to reality. I assume that there is some sort of decompression that occurs to bring him back safely. It is not shown in the movie, the ending intentionally left ambiguous.
Let's go with the notion that Rekall is a professional company, to have a implant program that kills you wife is,as you pointed out,potentially traumatic and very problematic.
Rekall would probably have a 'counter implant' program to mitigate the long term effects and trust issues once the scenerio is completed.
If the company didn't have this in place, lawyers would have a field day and the company would be toast.