I suspect that a Concentration check against a readied Magic Missile to disrupt spellcasting would ACTUALLY force 5 concentration checks at a very low DC for each. Hitting someone with 5 magic missiles and hitting them with 3 sword thrusts should be the same thing. You wouldn't add up the damage dealt by 3 sword thrusts to generate the DC. You'd generate 3 separate DCs.
For each incidence of damage taken, a character rolls a concentration check, DC 10+damage taken+spell level. In the case of a magic missile, this would be about 15+spell level - a joke for most casters. He would have to make 5 checks to keep it from disrupting his spell, but even a 1 rolled on a d20 from a guy with max ranks at 12th level with a decent CON would nearly always make it. Say enemy spellcaster has a CON of 16 and he's got 18 ranks in Conc. So he's got a +21 on Conc checks. 5 magic missiles, even maxed, wouldn't cause him to fail a spell of less than 7th level, even if he rolled a 1 on one of the checks.
Does this make sense? I know that the FAQ had said that you make ONE roll and apply the result to ALL generated DCs, but I thought I read in 3.5 somewhere (can't recall where) that you make a check for each instance of a created distraction.