Dear Querist,
Potential arguments in facts & circumstances of your case, which are without prejudice to each other:
A. As you have never challenged interest-liability & its quantum, Dept. should not have issued subject SCN in view of Section 79(3). Dept. should have simply asked you to pay interest and if not done, directly start recovery proceedings u/s 79. As entire SCN itself is invalid, there is no question of penalty u/s 73(11). Kindly pay interest first using Form DRC-03 and attach the same with your reply.
B. One can argue that penalty u/s 73(9) read with Section 73(11) is NOT mandatory as same is neither a fixed sum nor expressed as a fixed percentage, but same is 'fixed sum or a a fixed percentage, whichever is higher' and then, plead for either or very less penalty considering very low quantum involved, using Section 126.
C. As there is no demand raised for 'taxes' in the SCN (as same is only for interest & penalty, as per your last post) considering Section 73(7), penalty u/s 73(9) read with Section 73(11) should not be levied as this is case of non-payment of interest only & not non-payment of taxes.
Please note that these should not be taken as my views / opinion per se. But same are just some line of argument/s if you want to contest the penalty. As jurisprudence of GST law is at nascent stage and still evolving, these arguments will be thoroughly tested in courts of law over a period in future.
Also, if any amnesty scheme comes in future (one cannot predict or to be sure about it happening, though many are hopeful), your penalty will be dropped. But, for that, you need to contest the penalty and keep alive through judicial means (i.e. by challenging penalty, filing appeal & so on).
These are ex facie views of mine and the same should not be construed as professional advice / suggestion.