According to Tolkien's letters in one of the more obscure collections, the Numenoreans reached a cultural height shortly before their fall that compared favorably with that of the Elves in Aman or at least Beleriand. I think this was intended to show that the two kindreds of the Children of Iluvatar were "equal" in potential in all ways, and the comparatively lesser achievements of Men were primarily the result of their far shorter lifespan.
I think it is interesting that the Valar themselves felt threatened enough by the invading Numenoreans that they felt impelled to call upon Iluvatar himself.
There are two possible explanations for this. One is that the Numenoreans had the military capability to actually defeat the Valar in battle. This seems unlikely, but is given credence by a reference somewhere (don't have the books with me on the road) to the Numenorean invasion fleet as being the greatest that ever sailed. Presumably this would include the fleet in which the Host of the West sailed from Aman to defeat Melkor at the end of the First Age.
The other, and probably more likely, explanation is that the Valar were capable of defeating the Numenoreans, but not without massive slaughter of them, and they were unwilling to kill that many of the Children of Iluvatar.
All this is also interesting because some of those (mostly fundamentalists)who want to draw a strong contrast between the treatment of magic in Harry Potter and Tolkien like to say that Men in Middle Earth don't use magic. Obviously, powerful magic would have had to be used by the Numenoreans in order for them to face either Sauron or the Valar in battle.
Tolkien says this in one of his Letters, forget which one. The Numenoreans at their end were, as far as might goes, very, very powerful. They *could* have defeated the Aman on a purely military level -- even the Valar themselves.
I think the reason the Valar called upon Iluvatar is not only the valid point you raised about killing so many of the Younger Race, but that they couldn't do so delicately enough to avoid probably destroying Aman and many Elves in the process. Witness the results of all their previous battles.
Iluvatar, OTOH, had no such handicap. He can be as widely or as narrowly destructive as He thought best. The action He took in taking care of the Numenorians was direct, powerful, specific, and very effective. Very Godlike, in other words. :)
Tuor