My teacher told has told me two things of relevance here.
When I first started Aikido he told me "Welcome to a life of Pain". I suppose he was right.
A few years later, when discussing the discomfort of sitting in seiza for a long time we were told. "The pain won't go away, what you will end up doing is changing your relationship with the pain."
I've paraphrased a bit, but he was right. Sitting in Seiza is still painfull but it's a nice pain and I don't fight it anymore.
For the rest, eventually (in a few days or weeks or months) Aikido will become less painfull or even positively pleasant. You won't notice the change, but one day you'll suddenly stop and think, "Hey, didn't this used to hurt?".