Interesting question, P.; I wonder what's behind it? Did you do this and someone called you out on it?
We visit cemeteries more than most folks of our generation, I think (both historic ones and current ones, since we go "visit the relatives," and my brother does a lot to maintain some precious family graves in one small cemetery).
I would not have an issue with anyone walking through a cemetery for exercise or otherwise. Jogging might depend -- some of the jogging gear I see on folks here is not what I'd consider appropriate to wear in a place where someone might be visiting a grave, so I likely would have a negative gut reaction to seeing that; jogging in something appropriate, and not within sight of a funeral talking place or someone clearly visiting a grave site, would probably not bug me. I think the key would be the walker or runner being very respectful and cooling it immediately when in sight of someone who is at a gravesite, and never doing it within sight of a funeral.
I know a lot of folks of the older generation would have a huge issue with this, though, and I think their sensibilities should trump any exercise.
We exercise a lot of courtesy at cemeteries and don't go there for exercise, but we do walk among (not directly over) the graves at times (which is essential to reach certain graves in some cemeteries). Still I would not be too worried by judiciously done exercise on the perimeter, on paths, but not immediately in the area of graves.
A lot depends on the particular cemetery, too. Some actually have rules against anyone jogging, doing recreation, playing ball etc. in them -- you might want to check that out and see if the cemetery in question has such rules. Others have paths around the perimeter that practically invite exercise.
If you are talking about going around a cemetery with the kids for a brisk walk that's dandy and it is a chance to teach your kids not to think of cemeteries as scary or strange places. It also gives you an opportunity to slow down a bit and show your kids the tombstones and discuss history and the lives of others, and the reality of life and death. Our daughter actually enjoys cemeteries and finds them peaceful and fascinating. Last weekend we went to a cemetery just to see the grave of the founder of her school, and to pay our respects there.