In just two minutes, Ajahn Brahm tells us with clarity and compassion how to deal with pain during meditation:
As he says, when the pain builds and builds, “It’s common sense: move.” Otherwise you end up like the guy with the double knee-replacement.
I’ll note that there is plenty of wisdom in sitting through discomfort, through itches, and through distractions of various types. Otherwise few of us would manage to sit still at all. But learning to see what is discomfort and what is pain that can lead to long-term damage is a process nearly all meditators must go through.
And remember, everyone is different. Some people are genetically more flexible than others. Some people have practiced yoga for years and can painlessly plop into full lotus. Others (like me) tend to run, which can have much the opposite effect on flexibility.
Along with everyone being different, everyone is going to give you advice based on their own limited experience. I encourage everyone to run because it makes me feel great. Because I run I tend to talk about running and know more runners and hear more stories about how great running is, so a little positive feedback loop forms. I’ve met people who were obese before they started running but then lost weight; I’ve met people who were injured from one thing or another recover through running. People who meditate or do yoga or anything else that is good will often have their own positive feedback loops. That doesn’t make them (or me) wrong, it just means we have a well-developed particular perspective, and there are other ways out there of looking at things.
So talk to different people. Try different things. Find out what works for you. That goes as much for meditation as it does for life.
For more, see this lovely short piece by Dan Cayer at the ID Project Blog.