The entire point of Wrex and Bakara is that they're going to beat the Krogan into something resembling civilized behavior so they don't wind up at war with the entire galaxy again. Assuming he's still alive in ME2 you can see him doing his best to reform Krogan society to something that isn't pants-on-head-retarded. That whole Tuchanka arc is less about the Krogan and more about Wrex attempting to save his species from itself. If Bakara is dead and Wreav is in charge, you can actually convince whoever would have gone up to deploy the cure to just walk away citing the fact the Krogan will continue to Krogan.
Leaving aside what was mentioned before about it being so rare they were almost a myth before they needed Banshees everywhere, inbreeding was the biggest cause, and naturally there's zero chance of inbreeding when an entirely different species is the father. One of the
planet descriptions in ME3 talks about a heavy emphasis on exogamy and an almost instinctual aversion to consanguinity happening.