I read the OP, and for a minute thought I had typed it myself and forgotten ...
I know the feeling bro. I have this same issue. After much thought and deliberation (plus some marriage counseling), I have concluded that the problem isn't running per se. It's the wife. If "running" were replaced by any other hobby that you enjoy doing without her, for instance "painting" "woodworking" "rowing" "swimming", the problem would be the same. This is because:
A. wife is a control freak and can't stand the idea of you doing something that she isn't in charge of.
B. wife is jealous because you are keeping fit and she isn't, but she wishes she could. although she'd never admit this and you'd be an idiot to say so.
C. wife doesn't like being the center of attention all the goddam time. princess syndrome or whatever.
See, none of these have anything to do with running by itself. I can make my running as invisible to my wife as possible by running at lunch from work. I sometimes even sneak my running clothes into my car in the morning so she doesn't know I go. But it doesn't matter. I can leave work and get home at the usual times whether I run or not and it won't matter. Because in her mind I should be spending that time on something more directly related to our family rather than myself. Even if i basically play hooky from work to run and don't impact the family at all.
I don't have a solution, but only respond to empathize. If you ever figure it out, let everyone know. Or better yet, write a book and get very rich.