Mere issuance of SCN by Dept. on any issue does not automatically mean that assessee is at fault. Past experience / records proves that the Dept's views - in majority of cases - are not upheld at tribunal & above level of courts but courts ruled in favour of assessee / taxpayer.
My legal interpretation/s are NEVER based on or influenced by what Dept's views & course of action (such as issuance of SCN) will be. My interpretation/s are based on, what I feel, is the legal position which will be upheld in courts eventually in given set of controversies.
W.r.t. subject situation under discussion, I am of the view that the assessee is on very strong legal ground to defend ITC so taken.
Note: It is always for the assessee (not only for issue under condition here, but generally speaking, for every issue where Dept. can have different / contrary views) to take final call, based on quantum involved, risk appetite, willingness to defend himself following judicial process (if so required) & so on.
These are ex facie views of mine, the same should not be construed as professional advice / suggestion. & I respect contrary views.