As I see it, the real problem isn't so much with magic missile; it's with the overall power curve for wizards/sorcs. The premise behind magic-users since 1E days has been that they're utter wimps at low levels, rising to demigod status at high levels. A 17th level mage in 2E was basically far beyond just about every other character class. This was supposed to be "balanced" by how you could knock over the same mage at 1st or 2nd level (the assumption never really held IMO, which is why I put "balanced" in inverted commas).
3E isn't as bad as previous versions of D&D were in this respect. A lot of the high-level spells have been toned down a lot, and the wizard class has been beefed up a bit at low levels, primarily through high Int granting bonus spells. However, the steep power curve is still there. (Among other consequences of this, note how a multiclassed wiz who splits her levels evenly is usually much less powerful than a single-classed wiz -- this is because the benefits of high-level spells usually outclass what you can get from more levels of another class.)
A side-effect of this steep power curve is that a lot of low-level spells are relatively weak. MM is a spell that breaks this power curve, which is why it appears powerful compared to them. However, I don't see this as such a major problem, because low-level wizards _are_ such wimps otherwise. It's no big issue if they have one powerful spell, even if it outclasses other spells. It's still not going to overshadow anything that a low-level cleric or low-level fighter can do. A wiz with MM _may_ overshadow a wiz without MM, but even that's situation-dependent -- and if every wiz has MM, then the question itself becomes moot.