I think the way TIM rationalizes most of these disasters is that a few dozen deaths are acceptable losses so long as they get viable data from the experiment. Even if that data amounts to little more than: "well *that* doesn't work!"
For the record though, I'm pretty sure it was only the Overlord project that had the subject breaking loose and killing all their guys. IIRC of the colonies and outposts you come across infested with husks, rachni and creepers, only the two former were the work of Cerberus and even then it wasn't their facilities. With the husks they were deliberately infecting an isolated population to see what happened and I'm pretty sure the outposts attacked by rachni were alliance military. Not sure if that was even deliberate or the result of a shipping error.
As for the creepers, those were shipped off world by exogenii and infested an outpost. The only time you see Cerberus with creepers is when you wipe out their main base, in which are indeed husks, creepers & rachni, but they were all contained and the base personnel alive and well...until you kill them all.