Should Return Necessarily Be Processed Even When 143(2) Notice Issued?

Central Board of Direct Taxes in its Circular No. 549 dated October, 31, 1989 [see (1990) 182 ITR St. 1] has advised the Assessing Officers to issue intimation under Section 143(1) before issuance of notice under Section 143(2) of the Act
However,the question "whether the return should necessarily be processed u/s 143(1) even when notice u/s 143(2) has already been issued? " hounts both the mind of tax practitioner and even A.O.
The answer to this question has been legally settled by Supreme Court in Commissioner of Income Tax v. Gujarat Electricity Board [2003] 260 ITR 84.

Would this judgement apply for the new preovisions of 143(1) and 143(2)?
Open discussion...