Paying for link removal is a conundrum since as you state the site owners probably feel violated and that you essentially got what was coming to you. I have chosen to pay a couple that had been de-indexed from Google and even so, one did remove the links and the other has not.
As to your other question on removing sites from your disavow list that have been cooperative and removed the links, from what I have read there is no harm in disavowing them anyway. The risk is that some site owners may not have properly removed the link and it may come back. They may have temporarily redirected it to hide it or they don't know how to remove it possibly due to an older platform. I would be interested to hear from experts such as Marie on this point.