Dear Shri Pawankumar Soni Ji,
Denial of ITC solely due to non-appearance of ITC invoices in GSTR-2A is strongly arguable case (specially for period before 09.10.2019 wherein these restrictions under Rule 36 (4) comes into picture) in my humble view.
And if you want to defend your non-liability to pay penalty u/s 74, I feel that you must be ready to defend your eligibility of such ITC on merits first. If you succeed, question of any interest or penalty does not arise.
But, if you agree to reverse / pay against such ITC along-with interest (which is treated as admission of non-availability of such ITC), from my practical experience, Dept. officer is - more likely than not - will also ask for penalty u/s 74 (5).
You need to take holistic call in such matters.
These are strictly personal views of mine and the same should not be construed as professional advice / suggestion.