Hadiya's conversion to Islam and marriage to a Muslim man triggered a 'love jihad' debate in 2016; it was put to rest by NIA in 2018.
It is understood that corruption allegations were also raised against George M Thomas by the district committee.
Shejin and Joisna on Wednesday made their marriage official.
NCM chairperson Iqbal Singh Lalpura said everybody has right to marry a person of his or her choice.
CPM's Kozhikode district secretary P Mohanan said Thomas's statement on the wedding of a Christian woman and a Muslim man at Kodenchery contradicted the party's position on mixed marriages.
Mar Joseph Pamplany refused to use the term 'love jihad' out of respect toward 'Muslim brethren' but said church empathises with parents whose daughters are 'trapped'.
Joisna Mary Joseph, whose marriage with a Muslim man has triggered a controversy in Kerala, appeared before the court on Tuesday morning.
The court issued the order on a habeas corpus writ filed by Joisna's father Joseph who has claimed that his daughter has been taken away against her will.
K Surendran met the parents of Joisna, whose love marriage to Shejin had triggered a 'love jihad' controversy recently.
The CPM hosted a public meeting at Kodenchery in Kozhikode to explain its position after its former MLA George M Thomas's 'slip of the tongue'.