As mentioned here by our Senior Partner that Marriage Certificate is not a 'conclusive proof' of marriage then i would also like to add few points here.
You can very well start any activity under Indian personal laws against him without Marriage Certificate but as you have mentioned he is a NRI then these activities will only remain in India and cannot harm a person who is sitting outside India.You can file any charges against anyone but during the trial you also need to have something to prove it so INDIAN LAWS work well for Indians living in Indian territory but not so easy for someone outside India.
As per HMA registration of marriage is not compulsory but our Hon. SC and NCW have been telling againg and again that marriages with NRI's be registered otherwise its impossible to do anything.
Please note Marriage is only a ceremony as per HMA but in rest of the world Marriage is a contract and relationship so if the court needs to bring your NRI husband to India then there should also be enough proof that you lived as husband and wife and there was cohabitation and it was not just a sham marriage ceremony for few seconds.This is also the reason the marriage officer need both husband and wife to be present to issue the marriage certificate.
If you have problems with relation then get divorce instead wasting time to prove the legality of marriage.