If+Past Perfect + would + base form or ... + base form of 'be' (+ verb + ing)? Mixed conditional!
Solution 1:
A crude answer might be— Because a certain action happened at some point in the past (if you hadn't frightened her), the consequences of that action are still continuing (the baby wouldn't be crying now). Thus, the tense switches between the progressive and the past Indefinite.
Of course, this is not to say that this version of the sentence is not correct— The baby wouldn't have cried if you hadn't frightened her. Here the implication simply is that the baby only cried when frightened and is no longer crying.