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If Obama believed, as he obviously did, that "the effect" of the Court's decision in Citizens United v. FEC would lead to the undue influence of corporate finance in national elections (an issue that bi-partisan Congress addressed through various legislation for over a hundred years - and with the Supreme Court finding no substantive constitutional infirmity with the legislative limitations), it was quite appropriate for him to raise it in the State of the Union address,if he wants legislation to protect against what he believes "the effect" would be.
He is a politician and head of State; to declare his vision on needed legislation in such a public forum is not only desired but required. Whether his political opinion is correct or not, he was elected to have precisely that - political opinions.
On the other hand, Associate Justice Alito is not a politician (at least, not by job description), and should not publicly weigh in on what the President (or any politician, for that matter) surmise the political impact of a Court's decision may be, except in the course of a matter presented to and decided by the Court.
The Court's role is designed to determine - without regard to political opinion - as in this type of instance, whether legislation on corporate financing in national elections contravenes any constitutional protections, if any, to those corporate entities.
The reason why we accept an Article III judicial nominee's silence during the confirmation process on the wisdom, or lack thereof, of types of legislation is that our judiciary is not expected to have preconceived notions on how issues should be decided. Members of the judiciary, unlike politicians, are constrained to make decisions based only on the record before them.
To the contrary, we expect our elected lawmakers to make decisions in the public's best interest, based on the legislative record, as well as speculative notions (presumably reasonably ones). We even applaud our elected lawmakers to make decisions which take into considerations letters we write to them, valid public opinion polls, and even pure value judgment (particularly if we share those values). We will justifiably abhor a member of the judiciary who makes decisions based on those factors - if those factors are not part of the record in a case before the court.
Judges should express their opinions on debatable and non-debatable issues, which may come before them, only when they have accepted jurisdiction to decide such issues. Of course, they may have - and, indeed, should have - political opinions, but we expect and require them to not express them in settings which may expose the the judiciary to criticism of being susceptible to politicization.
In short, respect for separation of powers, adherence to the principle of judical restraint, and a commitment to promote the impartiality of the judiciary all compel the ineluctable conclusion that Associate Justice Alito should not have engaged in what amounted to a stealth presidential debate over what may be the effect of, in President Obama's political opinion, the majority's judicial opinion in Citizen United