The two-time president of BJP in Kerala made the remark while releasing a revised version of 'Gandhi vs Godse' in Kollam.
Tushar Gandhi made the comments on the eve of Mahatma Gandhi's 75th death anniversary.
The Mahatma's great-grandson writes that under present circumstances, the term Sanatani Hindu conjures up a very scary picture.
The country on Sunday paid tribute to the Father of the Nation Mahatma Gandhi on his 74th death anniversary.
During a 'dharma sansad' at Raipur in Chhattisgarh on Sunday evening, Kalicharan Maharaj had allegedly used an abusive word against the Father of the Nation and hailed his assassin Nathrum Godse.
Questioning the freedom movement led by Gandhi, Hegde said it was an 'adjustment' with the British and freedom fighters had asked the British to imprison and 'properly take care' of them.
Congress ally Shiv Sena and rival BJP attacked Congress on the insinuation by its frontal organisation.
Thakur's apology came a day after opposition benches demanded an apology from her and submitted a censure motion signed by 50 MPs to Speaker Om Birla.
Thakur created a controversy on Wednesday with her remark in the Lower House during DMK member A Raja's narration of a statement by Nathuram Godse before a court on why he killed Mahatma Gandhi.
Even during the Lok Sabha election campaign, Thakur had described Godse as a patriot, triggering a huge political storm.