What if Eli Wallace wasn't the first in his family to be linked in Stargate Command? Okay, it's highly likely that them choosing him was completely random during the prometheus game puzzle, but i found other Wallaces in the Stargate-verse.
Henry Wallace was the president of Devlin Medical Technologies, who had a daughter Sharon Wallace in SGA. Perhaps Eli's absentee father could have been this guy for all we know and Stargate Command got wind of Eli's intellect (much like the old man). kind of makes sense.
Another theory of how Stargate Command was alerted to Eli's presence could have stemmed from yet another Wallace under the command of John Sheppard in SG-4 called Major Christopher Wallace (a cousin perhaps?)