"I am appalled at the crude and barbaric spectacle of certain former students of the college hounding a man of proven integrity and stature like Thampu.
"This witch-hunt began, as I remember, in 2007 when he announced the admission policy, affirming social justice in higher education," Agnivesh said in a statement.
A group of St Stephen's alumni have alleged that Thampu's appointment was illegal after questioning his qualifications for the post. They have also charged that Thampu was responsible for "rampant misadministration" in the college.
The alumni group has also alleged that the college is deliberately hiring only Christian teachers.
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However, St Stephen's Supreme Council, its top decision- making body, has passed a resolution saying the "alumni have no right to interfere in internal matters or administration of the college".
Thampu recently came under fire for suspending a student e-zine in March for not seeking his clearance on its content before the edition's publication.
"I call upon all concerned to stop this barbaric witch- hunt and to leave St Stephen's unharassed (sic) to pursue the great service it has been doing these many decades.