I'm afraid the worried mother detail is brought into question on two points.



1. She chose a very high profile target and put her children directly in harm's way for the purpose of conquest. Celestia did not know Chrysalis, so this may rule out that she attempted to appeal her case through more peaceful means. While sounding dull, it is brought into question how motherly or fatherly one's behavior is when they expose their children to potential danger when it is a question of whether or not it is necessary to do so (stronger possibility she did not attempt more peaceful means to present her cause before resorting to more extreme means). What is not into question is her intention to conquer (there may or may not be a solid reason for this later revealed). The comics made it pretty clear she is quite obsessed on conquering multiple kingdoms.



2. Both in the comics and in the show, Chrysalis didn't seem that moved when her changeling army was being attacked directly (ponies defending themselves from them). Mind you it is plausible that a person in that position, in which their children are trained to defend themselves, expect a certain degree of potential harm to come their way, but not being moved (expressing verbally or nonverbally being bothered over personal loss coming to her own) does bring the concerned mother theory into question. She seemed much more occupied in dominating her victims than what happened to her changelings (it may be interpreted that her caring more about the state of being of her victims than the state of being of her army may speak in its own right).



EDIT:



For #2, a good comparison may be how Shining Armor would react if his troops were seriously hurt, how Luna would react if her troops were seriously hurt, and Celestia made clear her reaction when she saw the threat Chrysalis posed towards her subjects.



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Anywho, that's my take. And actually, if it is accurate that Chrysalis cares more about those she victimizes (and how much) than those she looks after, this could send a strong message to the changelings that could go one of two ways.



1. The changelings become genuinely upset upon realizing this and some of them defect. Not much changes on Chrysalis' side, as a good number of changelings would find reason to defend her (either not wanting to leave anyway, and/or still thinking she really does care about them on the inside and still has yet to show it more outwardly).



2. Both the changelings and Chrysalis become aware of this. Chrysalis genuinely apologizes and becomes more cognizant of the changelings, and makes efforts to boost morale and otherwise increase loyalty. The bond between her and the changelings grow more strongly, and the purpose of this one would be to show a redeeming quality of a villain (has evil aims, but makes it clear that they care about what happens to their followers).





Anywho, that's my take. If you have rebuttals for point #1 or #2, feel free to post.