I think the takeaway here is that WBgames probably said "there's a market for our fighters on Vita" regardless of what the profit margin was. 250k copies is nothing to laugh at when people are doubting the install base and viability of the Vita overall.
Maybe the port cost them peanuts and they did it as a proof of concept. If they think they can get Injustice going on there and the sales from MK lead them to believe that Injustice will move copies at $40 a piece, let them go for it. I don't want the game personally, I'm not a fan... but if it gives other Vita owners something to buy/play/etc... great, bring it over.