Really? Because to me, Natasha seems to be pretty much judging Maria on current operational issues, not things like Civil War etc, etc. (well, there was that one bit about the 'right side' last issue, but I read that as more whether Maria is working for Osborn) Maria's supposed to be a top-notch field agent, she's coming in with an urgent message and unknown tech from Tony Stark... and at the same time, she's doing it in a rather ridiculous and overt way. Seriously, painting Natasha's logo on the front door of her building?
To me, Natasha's simply being practical and trying to get something approaching a proper SHIELD agent out of Maria. (In a panel not shown here, the phrase 'best agent of your generation' is thrown out). They are in a bad situation, with very bad people coming after them, the stakes are high, and the current Maria is likely to get them both killed in action. (And honestly, yes, Maria is suffering from post-mind-rape trauma... but she's still a high-end agent of SHIELD. If anyone should be able to bounce back from this sort of thing...)