Essentially, they chose to act secretly, and outside the customs & laws of the WT, because they felt they couldn't trust the rest of the Tower. Regardless whether or not it was the wisest course of action (and I tend to think it was), the rest of the WT could not possibly tolerate an Amyrlin who acts outside the rules AND who doesn't trust them. Siuan and Leane were well aware of that, and knew perfectly the consequences if they were caught. It was a calculated risk, and ultimately they had to pay the price.

Of course, their punishment could have been handled better, but they did deserve it. Actually, I don't think either of them question the validity of their punishment (the deposing and stilling part), they just resent how it was handled, and Elaida's involvement.