An earlier Supreme Court judgment had barred the government from appropriating or reserving any seats in unaided private educational institutions but the subsequent Constitution 93rd Amendment enables the state to extend reservations to them as well. This has not been done though, and without a challenge, the Supreme Court has left the question open. The exclusion of minority institutions from the ambit of reservations, however, has been upheld on the ground they are governed by a separate constitutional scheme.
It is correct that the CJI K.G.Balakrishnan's opinion does carry language to that effect but three of the other judges explicitly stated that they were not addressing the question and the fourth (Dalveer Bhandari) chose to strike down a different part of the provision. Altogether in any case, the ratio was not met (3 votes were required for it to have the force of law) and if challenged in the future, the law as a whole is certain to reviewed and there is a fair chance that the entire law including the portion excluding admissions to minority institutions from the ambit of state regulation would be struck down. The Hindu therefore appears to be reading too much into the Chief Justice's words (is it being too anxious to protect this minority privelege?) which ought to be considered as no more than obiter dictum.
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