Some people could potentially find this offensive. They're unlikely to be offended enough to say anything to you, but never the less may not appreciate their loved-ones place of rest being used as an outside gym. You should find another place to go running. The cemetery is neither the only place to run, nor the most appropriate.
On the other hand, what is and isn't appropriate is entirely subjective. I know I'd be happy for someone to run by my grave, and ideally I think cemeteries should be beautiful enough that people want to go to them for reasons other than to morn. They should be happy places. Not sad. If someone disagrees, that is ultimately their problem. So long as you're not doing anything otherwise objectionable while running (you're sticking to paths, not littering, etc) you should continue to run in the cemetery.
https://charliehalloween.zenfolio.com/img/s/v-3/p1283445150-...
That said, too small to run.