I sympathize with you. You got caught in the ill-communicated, permanently and always-last minute changing and never coherent Thai immigration mess. Add extra bad luck to this with you getting covid.
I am not really sure what to advise in this special case / what the best course of action is. Usually, overstay is never a desirable option.
Then again, the question is: Did you notify the officials when you tested positive for COVID? I am asking, as not doing so is illegal in Thailand and may come at additional problems and fines.
If you did report covid: I would go to immigration now and settle it.
If not, one could consider sitting it out on overstay.
I hope someone can give you more helpful advise. Maybe
@Stu***
?