First of all you need to realize and accept that there are some stereotypes against white people and especially white girls. Now the fact that you and your boyfriend are atheist (I'm guessing he is clean shaved) doesn't really help this so much. If you were to ever get married it's likely that your kids won't accept Sikhism and this might be the reason why his mom cried. She sees you as a threat to the culture and religion this family has followed for so long.
My Suggestions: Don't send her flowers. Instead learn a about Sikhism and appreciate it. When talking to his mother, If you mention the sacrifices given by Guru Arjan Dev Ji and Guru Gobind Singh Ji and you show that you really appreciate their sacrifices for humanity (which is very easy to appreciate) it would hopefully have a better impression on them. But don't make it look like you're doing this just to impress them...
Drug free, no kids, well mannered.
This should further strengthen their trust for you and show them that they'll be lucky to have you in their family.