Accepting a scholarship for masters just to get the money and fund a future masters I have been offered a scholarship for a masters in theoretical physics at my home university, the scholarship covers the fees along with a decent stipend but I would rather pursue a masters in maths at a different university. 

I feel alot of pressure to take the money for finical reasons but ultimately its not what I want to do. Part of me is considering accepting the offer and using it to save for a masters in maths. I feel I will be at a disadvantage trying to do a PhD in mathematics if I take this scholarship since I will have effectively spent 2 years of my prime going doing the wrong route. 

If do a masters in maths I will likely have to take out a loan of about 8000-10,000. I'm afraid this will be too much to pay of with a PhD stipend and result in me having to work for a year or two again delaying my career. 

Would the time spent doing a masters in theoretical physics put me at a disadvantage when applying for math phd's?

Do typical PhD stipends have enough room to pay off loans?
First, my advice is to never think of a graduate school stipend as a way to earn a living (or to save for future goals). Stipends are design to barely cover minimum costs of living, and often fall short of that goal.

Second, I'm not sure whether a Master's degree in theoretical physics will help or hurt an application to a maths Ph.D. It seems that it could be related, depending on the subfield of maths that interests you. 

Third, in many fields you can apply to Ph.D. programs directly without a completed M.S. degree first. Maybe that is also possible in your case.