Is this true, or is it post-hoc rationalization? A bit of both.
For one thing, Bush's plan to put GBI complexes in Poland and the Czech Republic was not meant to defend Europe. Rather, the initial discussions of a European missile-defense plan, in 2003-04, focused on using these weapons to shoot down missiles launched by Iran as they passed over Europe on their way to the United States. The interceptors could provide protection for some parts of Europe, but that wasn't the main intent.
So, yes, to the extent the SM-3s work, they would protect Europe more than Bush's plan would have. Whether they work—whether they really can shoot down ballistic missiles—is another question. Certainly, short-range missiles are easier to shoot down than ICBMs: they travel more slowly, their trajectory is easier to track, their warheads are smaller, meaning there's less room for decoys or other devices to throw off the missile-defense system's radar.
In some ways, though, the question hardly matters. Obama has made little secret of his skepticism about the missile-defense program as it existed under the Bush administration. He has said, in past speeches, that he would support a missile-defense program if it proved effective in tests, knowing full well that the program—the larger program, involving the GBI complexes—has performed rather poorly in tests. (The SM-3s have done better against short-range missiles, though little information has been released about the precise design of those tests.)
Obama also clearly wants to revive relations with Russia—a goal that he and many of his advisers view as critical to the success of his broader policies to fight global terrorism and to curb nuclear proliferation. The plan to put missile defenses in Eastern Europe was seen by the Russians as a threat, an attitude that isn't unreasonable from their point of view. It seems silly to throw a wrench in this relationship—and thus sharply reduce the chance of success in these vital areas—in order to preserve a missile-defense system that doesn't seem likely to work anyway.
However, it is impolitic—it risks rousing accusations of being "soft on defense" or worse—for any president (or most senators and House members) to say out loud that missile defense isn't likely to work and that, therefore, the program should be scrapped. (I'm not saying that Obama thinks this; I'm saying only that if he does think this, he couldn't say it.)
Obama's plan—scuttling the GBI complexes in Eastern Europe and instead putting more SM-3s on Aegis cruisers, which can be put in the Mediterranean or anywhere—manages to undercut the Russians' rationale for continuing their intransigence while, at the same time, it assures the Europeans that the United States will continue to provide a defense against missile attacks, that it will in fact do so more quickly and effectively than the original plan would have.
Still, two questions remain to be answered.
First, what will Obama do to provide special reassurances to the Czech Republic and Poland? To the extent that their people fear a resurgent Russia's aggression (and, given the history, such fears aren't out of line), those big, fixed GBI complexes would have been a tangible token of American commitment to their defense. The NATO treaty's obligations are one thing, and hardly trivial, but the presence of a strategic asset, like a missile-defense complex, would guarantee full protection from—and therefore stand as a potent deterrent to—an attack or intimidation by Russia.
This doesn't mean the United States should install the complexes, whether in Poland and the Czech Republic or in any other country that desires a security umbrella. The Turks were disappointed in 1963 when President John F. Kennedy dismantled the 15 Jupiter nuclear missiles that had recently been deployed there. (It was a secret at the time, but he did this as part of the deal with Soviet premier Nikita Khrushchev to end the Cuban missile crisis.) He assured the Turks that a new Polaris submarine, armed with 16 nuclear missiles, would be stationed in the Mediterranean instead. To the Turks, this wasn't the same thing: A Polaris could move away, a Jupiter couldn't. But surely Kennedy did the right thing. Those 15 Jupiters weren't worth risking war with the Soviet Union, and the Polaris was a much less vulnerable, and therefore more effective, deterrent.
At least in the current case with the Czechs and the Poles, the GBI complexes haven't yet been built: Obama isn't dismantling anything; he's merely saying that he's not moving forward with the previous president's plan, which was always controversial. Still, he should devise and offer some set of extra assurances.
The second question is more important: What will the Russians do now? They've cited the missile-defense plan as the main source of suspicion, the main obstacle to improved relations. Now that Obama has wiped it off the board, will Putin and Medvedev come around—or will they bring up some other reason, some other excuse, for remaining distant and occasionally hostile? It's in the Kremlin's court.