I am asking for something, if there is anything at all, that can prevent the damage on a hit; not concealing or any other situation in which the caster wouldn't be able to target the creature.
Well, there's shield, of course, as well as the brooch of shielding. Lesser globe of invulnerability works (as does similar spells), as does an antimagic field, the spell Nightshield (Spell Conpendium 3.5), Spell turning is an option 2 I think .
You can counterspell it with magic missile or dispel magic. A ring of counterspells can be used by non-casters.
You can boost your spell resistance to negate the spell.
Mirror image or any other spell/effect that makes you seem to be in one place rather than where you are can be useful as well. However, blink, et. al., do not work as force effects extend into the ethereal plane.
There are a variety, but the most common by far is the 1500 gp brooch of shielding. Does not require actions or spellcasting ability to use and has no duration. Can be put on fighters, pets, etc.
Readying and then casting the 3.5e Telekinesis spell as a Violent Thrust can hurl one object per caster level.
Not only would this prevent the magic missile damage, the spellcaster could then redirect the magic missiles towards the enemy spellcaster or another target.