I'll begin by putting aside Scalia's historical and doctrinal arguments (except to say that I think he overreads Ex Parte Bollman). The textual argument (made by both Scalia and Gonzales) strikes me as especially weak. Although it is logically correct to say that a prohibition on suspending something doesn't guarantee that that something must exist, it certainly is a common sense inference that if X can't be suspended, X must therefore exist.
So let's turn to the normative argument. Scalia says:
It is no more irrational to guard against the common and well known "suspension" abuse, without guaranteeing any particular habeas right that enjoys immunity from suspension, than it is, in the Equal Protection Clause, to guard against unequal application of the laws, without guaranteeing any particular law which enjoys that protection. And it is no more acceptable for this Court to write a habeas law, in order that the Suspension Clause might have some effect, than it would be for this Court to write other laws, in order that the Equal Protection Clause might have some effect.The analogy Scalia draws to equal protection doesn't work. It is perfectly understandable for members of group X (women, say) to feel wronged when members of group Y (men, say) get some benefit that they are denied, even if the X's would not be injured by the denial of the benefit to everybody. That is simply what we mean when we ascribe normative content to equality.
But is it ever the case that people are worse off when some benefit (I don't say "right" to avoid begging the question) is denied to them temporarily than they would be if it were to be denied to them permanently? I suppose we can imagine that people might become "addicted" to the benefit if it were granted, then taken away, then re-granted, and so forth, so that they'd be better off never receiving the benefit. So if the American people were like the bears in Yellowstone National Park and habeas corpus were like food, Scalia could say that a temporary suspension is worse than a permanent abolition because in the latter case we don't come to depend on habeas, only to have it snatched away. This is a ridiculous analogy, however, and Scalia does not make it at this level. Instead, he simply asserts that protection against suspension is like the requirement of equal protection, even though it plainly is not.
Moreover, there is a further, to my mind independently fatal, difficulty with the Gonzales/Scalia view that Congress can "permanently" abolish habeas (for some class of cases) without implicating the Suspension Clause: As I say in the column, there is no such thing as "permanent" legislation. Congress can "permanently" abolish habeas one day, and then "permanently" restore it the next. So the answer to the question of whether any sense can be made of the Gonzales/Scalia view is no.