No, I would not recommend getting a Master's in Exercise science. I would recommend working on strengthening your application and finding out why you didn't get accepted to any schools. For example, if you got a C in any of your science classes, I would retake it at a community college. If your GRE score was low, retake it. You can also spend this year getting more PT experience and work a full time job that would help pay for your tuition for PT school.
I'm saying this because I just got my Master's in Kinesiology. At the time, I was unsure what I wanted to do after I finished my undergrad. I applied last fall and got into several schools. I don't think I got in because I was pursuing a Master's Degree, but I got more PT experience, work experience, and I retook one of my science courses to raise my pre-req and science GPA. That grade for that one science course really killed my science GPA, so retaking it made a huge difference. I never heard of any schools that waive requirements if you got a Master's Degree. I also thought to myself that if I didn't get accepted to any PT schools, that I would have my Master's Degree as a backup....except even with a Master's Degree in Kinesiology, there are very few jobs out there, unless you wanted to do research and get a Phd. That's my 2 cents.