The Triple Talaq case involves lots of specific complications that may distract from the question, but those complications suffice to show that the courts do not face a paradox. The Muslim Personal Law (Shariat) Application Act, 1937 previous applied, so that if a couple was married under Muslim personal law, the husband (alone) can unconditionally divorce his wife by saying "talaq, talaq, talaq". This plainly violates Art. 14 of the constitution (the analog of the "Equal Protection Clause").
The intrinsic contradiction is that there are special laws for Muslims, and special laws for Hindus (which were passed before independence and the writing of the constitution). In this specific case, one basis for overturning the law is that it is manifestly arbitrary ("What is manifestly arbitrary is obviously unreasonable and being contrary to the rule of law, would violate Article 14"). It was also found that talaq-e-biddat violates Islamic law. Insofar as this was a 3-2 vote against section 2 of the Muslim Personal Law Act, there was not a unified rationale, and the only thing that is clear is the concrete outcome: talaq-e-biddat is now against the law.
As for the question of allowing religion-specific laws, the concept of secularity arises in two places in the Indian Constitution. First, the preamble states that "We, the people of India, having solemnly resolved to constitute India into a sovereign, socialist, secular, democratic, republic...", and Art 25(2) says
Nothing in this article shall affect the operation of any existing law
or prevent the State from making any law (a) regulating or restricting
any economic, financial, political or other secular activity which may
be associated with religious practice
There is no violation of the principle of secularity by requiring the conditions for divorce to be uniform for all Indians.
As is universal in common law countries, the Supreme Court gets to say how the constitution is interpreted. I do not have any idea what Nehru thought "secular" meant, but I doubt that he had a peculiar belief that "every pressure group is entitled to legal immunity from the law of the land". Rather, "secular" means in India what it means everywhere in the English-speaking world. He may well have had unique ideas about what laws ought to be, in order to bring about a secular nation: it's pretty clear that he did not believe in special legal treatment based on religion. So an "originalist" argument in support of letting one religion pass its own laws for its people would not pass constitutional muster.