Hello,
1) There's no impediment to marry under provisions of Special Marriage Act even if they are married through a nikah. Divorce will always be governed by provisions of the the Special Marriage Act.
2) He will have to get a divorce from a court to be able to marry again. The provisions are meant to help people marry inter religiously without having to lose their original status.
3)A change of religion can cause him to lose his benefits rising out of minority status.
4) Once they are married under Special Marriage Act, triple Talak will no more be applicable.
5) It's highly advisable to allow them to marry under provisions of Special Marriage Act and stop worrying much and interfere much in the decision of two adult individuals. The more that you insist about a conversion the more you end up imposing conditions in the relationship and tension and misunderstanding in their lives and these can become counterproductive.