In this context, you should read the word "deformation" as "change in shape". Please do not read the word "deformation" as "a change in shape for the worse". In some cases a permanent (plastic) deformation of muscle tissue can be beneficial! For example, if you have tight muscles and you are able to relax them with yoga poses. If the effect were not permanent and plastic, your muscles would be tight again after you finished your yoga session.
The scientific research that Mukunda quotes shows that low-effort, long-duration stretching is more effective than high-effort, short-duration stretching for this purpose. It makes a strong case for yoga ("relax the effort") compared to more strenuous exercise.