Praise be to God.
Actually, you misunderstood the verse.
”O you who believe! Take not the Jews and the Christians as Awliyaa’ (friends, protectors, helpers), they are but Awliyaa’ of each other. And if any amongst you takes them (as Awliyaa’), then surely, he is one of them. Verily, God guides not those people who are the Zaalimoon (polytheists and wrongdoers and unjust)”
In here it means that you can take a Christian or Jew or any kind of disbelievers as your best friend with the following conditions:
-Your Christian or Jew friend should not be taken against Muslims
-You only can take Christian or Jews as your friends who do mock or make fun or insult any element of Islam.
Note. Also prophet Muhammad married a Christian woman name Marie and then she became a Muslim. So according to this, you can be friend with anyone you wish, either with an atheist or anybody you wish. And of course, when we read a Hadith, we need to try to understand it instead of misunderstand it.
Conclusion: If your disbeliever best friend mocked or made fun or insulted one of the elements of Islam, then you should abandon your disbeliever best friend unless your disbeliever best friend repents to God sincerely, then you may continue your friendship.
And God knows the best.
End quote.