The free dictionary defines presides as
pre·sid·ed, pre·sid·ing, pre·sides
1. to sit in or hold a position of authority, as over a meeting
2. to exercise authority; control
For a layman like me; Headline would mean Zadaphia told SIT Modi oversaw (or lead) the riots.
In the body of the news TOI, what exactly Zadaphia told SIT
Zadaphia has told the SIT that it was Modi who kept in touch with senior police officials and bureaucrats during rioting. The former minister alleged that he was sidelined by Modi and was not called for official meetings which were conducted by Modi during the riots.
So Zadapia had actually told SIT that Modi presided during the riots and he called police officers. I am not sure if that’s a crime. Isn't leader of state take direct control over affairs during such an crisis and if I am not wrong Narendra Modi was also the Home Minister in 2002. Isnt it logical that Minister of Home and not his junior (mos for home) presides over meetings