You have to do what’s best for you at the time, and obviously taking the morning after pill was the right decision for you.
I don’t know that much about the morning after pill specifically, but I wouldn’t worry about long term issues. Yes, it’s going to stir your hormones up for a while, and obviously that’s not the ideal, but it’s also probably not going to do long term damage.
I would try to make sure you are getting the same nutrients that the COCs depelete as well as making sure you give your liver a little extra support so that it can get rid of the excess hormones.
I don’t know if you have seen my post on coming off hormonal contraception?
That has some advice on nutrients and liver support. Good luck, and I hope you are back to normal quickly :)