When the matter was taken up by the special NIA court on Monday, the three accused filed applications through their lawyers seeking exemption from appearance.
Mahindra's comments in a tweet come amid a controversy stoked by BJP's Bhopal candidate Pragya Thakur, a terror accused, praising Gandhi's killer Nathuram Godse as a patriot.
"It is natural when the BJP fields (a person) accused of terrorism and those (who) indulge in the politics of communal hatred. It would be better had the nomination of such candidates was cancelled for safeguarding the ideals of democratic values," he tweeted.
Bharti, who is not contesting the election but has won from Bhopal in the past, was seen consoling Pragya Thakur, who was seated in an SUV, wiping her tears.
Thakur is in the eye of a storm for controversial statements that her "curse" led to former Maharashtra Anti-Terrorism Squad chief Hemant Karkare's death in 26/11 Mumbai terror attack and that she was proud to have participated in the 1992 demolition of the Babri Masjid in Ayodhya.
The father of one of the blast victims moved the court Thursday, urging it to bar Thakur, the prime accused in the case, from contesting the election from Bhopal.
"Malegoan blast case accused and BJP candidate from Bhopal Sadhvi Pragya is claiming that she is contesting a 'dharm yuddh'. This is the real face of BJP/RSS which is being exposed continuously. But why is the Commission only issuing notices and not cancelling the nomination of BJP ratna (gem) Pragya?" Mayawati tweeted.
Will uncommitted voters support or be put off by the BJP choosing her?