According to the Something Awful playthrough thread for the game:

Because of the intricacies of the Japanese game rating system, blood in this game is colored pink. Rest assured, though, it is human blood you will be looking at, and it doesn’t mean our characters are secretly aliens or elves.

TVTropes also says the same thing:

Many murder scenes are liberally splattered in Pepto-Bismol, thanks to the intricacies of the Japanese game rating system.

So it seems like making the blood realistic would have given the game a higher age rating, possibly restricting some of their target demographic from being able to purchase the game. But the pink blood also goes along with the main artistic style of Dangan Ronpa.

According to Wikipedia:

The game uses pop art, a bright and colorful style, as a way to contrast the dark subject matter of murder. Scenario writer Kazutaka Kodaka stated he desired to “…shake user’s heart by showing a devastating accident in not devastating ways. But, by some measure, it might be more shocking than showing a devastating scene.”