Damn, just typed a long post and somehow it disappeared!
Anyway. to abbreviate, which is probably best anyway!
Pain does not have to be a part of it. Most of us in the west have not developed our bodies adequately in a way to train in martial arts, or an art such as aikido.
To do the things that are required of the art, we need to have pretty good core strength.
You must be able to squat down to seiza with good posture, stand back up, pull your center from your core, use your hip flexors, maintain good spinal alignment...and all that stuff.
I observer most beginners and I really think that we through them out there on the mat doing this stuff with little or no good conditioning.
We think they cannot do these things because they simply need to learn the moves. What I observe many times is that they simply have not developed the core strength to do them correctly.
Unfortunately, If we took the time and told them to "go do these exercises, and come back in a year". we'd have an empty dojo!
So, they endure the practice as best they can, "cavet emptor" and hope that they do not get injured backs, necks, or torn rotator cuffs from losing their balance and falling wrong, oops I mean taking ukemi!