Hello,
1) As the builder has not fulfilled his part of the contract he can not dictate terms to you.If there are illegalities about the construction he is responsible to get them regularised and is liable to get you the 'clean OC'.
2) You can write to the builder to give you clean OC and also rectify major defects occurred in complex due to poor quality materials used. In case he is not taking appropriate steps and is adamant in his stand that "Warranty period will be from the date of occupancy", issue him a legal notice regarding defects in the building and the illegalities.
3) There is no guarantee that the PIL will be decided in favour of the builder and therefore you need to initiate steps against the builder to protect your legal rights.