Can one atone for the sin of intentionally killing a cat, and will one be held accountable for this action on the Day of Judgment, even with sincere repentance and an abundance of good deeds?

A sincere repentance, with its conditions fulfilled, erases the effect of a sin, even a major one, as if it never occurred. So, whoever repents to Allah and regrets what he has done, that is sufficient for him, for Allah has not imposed upon the sinner anything but repentance.