Salamun Alaikum,
What is often overlooked in verse 2:221 is the fact that it is not so much the 'category' of people that is of focal concern but equally importantly, the 'reason' why.
Marriage is not viable from a deen perspective until 'aman' (belief) is established (hatta yu'minna - until they believe). Even a 'mu'min' (believing) 'slave' is better in marriage.
If this stands true for a 'mushrikeen', it is incredulous to assert that 'disbelief' in God outright (atheism) would not require the same premise for marriage (belief). As an example, if any text disallows one to strike one due to the possibility of injury, it certainly implies that beating is out of the question. This is just rational deduction.
The Quran encourages believers to seek the best meaning. It doesn't take much to deduce what the best meaning would be given the narratives of the Quran in this particular case.
039:018"Those who listen to the Word (the Quran) and follow the best meaning in it: those are the ones whom God has guided and those are the one's endowed with understanding"
With regards marriage with people of the book, please see my article below.
http://quransmessage.com/articles/marriage%20with%20people%20of%20the%20book%20FM3.htmRegards,
Joseph.