Although I may be corrected regarding this as it is based on my own subjective interpretation of the scene (which I have seen on multiple occasions since its 2006 release), I have always taken this as an example of the absolute and unconditional prejudice Cap. Queenan and Dignam have towards the idea of Costigan making a career for himself as a State Trooper. Due to his family background, they seem to have both a personal and institutional bias towards his progression and as such, they use what they see as the inevitability of his non career to coerce him into suiting their agenda in using him as for the undercover operation on Costello.
The SAT score appears to ultimately have nothing to do with any of this. His score could be 1400, 700 or 0, he could take or refuse the undercover assignment he has been offered but regardless of any of these outcomes the 'brass' appears adamant that under no circumstances will Costigan make a career as a Massachusetts state trooper.
(this is entirely opinion based and as such I would not be surprised if it were closed, but I hope it provides at least some food for thought in the interim)