Going by India's style of functioning, India is likely to treat the two issues (nulear and gas pipeline) seperately. The LNG price negotiations will be done on purely economic terms and the Nuclear row with IAEA will be treated as a geo-political issue and will merit a seperate set of geo-politico-strategic consideration on part of India.
That's understandable. The USA tends to do the same--that is, trying to separate economic foreign relations from security concerns. See our leaders' sometimes shameful treatment against Taiwan in favor of China's vanity and penchant for expansionism, for example.
Even military action against Iran would not be likely to interrupt the pipeline construction. If India wants to follow through with the pipeline deal, it will happen.