I will have to agree with the others. There is always a chance of injury, but statistically, you have a higher chance of getting injured playing golf then you do martial arts. Strange, but true.
An important thing to remember is that you can't train in aikido without experiencing some level of discomfort or pain. How else do you know how it feels and how to do it? The level of pain in mostly
determined by you. Keep in mind that you can always tap if the pain is too much.
You also asked about iaido, well I have a knee that bothers me. In iaido, you tend to do a lot of forms from seiza (sitting). There is a lot of up and down motion involved (rising & returning to seiza), sliding on your knee(s), etc (aikido has a lot of the same motions as well). I can tell you that some days my knees are pretty sore. If you were to wear knee pads, that may minimize or eliminate that problem (just ask your sensei). Now, most of the sitting forms do have standing forms that are quite similar, but most start from seiza if able to do so.
As far as harmony.... I don't think that is the main focus of class. I would say it is more of a bi-product. You just sort of understand after taking classes for a while. My best advice for you would be to actually go, sit and watch a few classes. This will give you a better idea of what actually goes on in the dojo you are wanting to join.