I don't see why it would be a problem. We're hormonally and physically similar to cis women, and the solution for a woman who doesn't like feeling weaker is to exercise to get stronger.
I got back into my exercise regime as soon as I could (which meant waiting a few months for the area to heal before I could go back to biking 10 miles or more at a time, but weightlifting was fine after 3 months), and I definitely felt better once I was working out again. I even think being in good shape was one reason I healed easily and quickly.
There's no reason it has to be running, either, if there's something else you'd prefer.