Dear Mubashir,
As-salam alaykum
Verse 3:28 that you have kindly shared as well others such as 5:51 cannot be read in isolation. This theme is clarified in other verses where the prohibition is only against those that are bent on making a mockery out of the religion and causing strife.
Please kindly note below:
005:057
"O ye who believe! take not for friends / allies / protectors (awliyaa) those who take your religion for a mockery or sport / ridicule or fun (huzuwan wala'iban), whether among those who received the Scripture before you, or among those who reject faith; but fear ye God, if ye have faith (indeed)"
The same word 'awliyaa' has been used but the context has been clearly elucidated against those who are deemed 'trouble-makers'.
Those who have never shown any difficulty or animosity whether from the People of the Book or Disbelievers, one is only expected to show them kindness and deal with them justly.
060:008
"God does not forbid you respecting those who have not made war against you on account of (your) religion, and have not driven you forth from your homes, that you show them kindness and deal with them justly; surely God loves the doers of justice"
As I trust that you will appreciate, many verses of the Quran are elaborated in other parts of the Quran and any 'summary' verses should always be understood in light of the more elucidatory verses.
I hope that helps, God willing
Regards,
Joseph.