During deep meditation, I often experience the bottom sides of my legs and pelvis region getting really tight. Sometimes it goes over to trembling and vivid shaking that tends to settle down in the end of the meditation.
I often read these spontaneous movements should best be smoothed/stopped in favor of the deep meditation. My question is: Isn't this just another form of purification that should be allowed for? Just let it happen?
Yes, these are symptoms of purification and it is fine to let them happen.
During Deep Meditation, all you need to do is to favour the mantra with your attention over anything else that is going on and return to the mantra whenever you realise you are off it.