From what I understand, she clearly understood the limitations of what Babbage achieved and wrote her program to demonstrate the value of extending the hardware in order to run more universal "programs," like the one she writes!

http://rclab.de/rclab/_media/analyticalengine/aal_noteg_glas...

Also note that apparently Babbage later did consider exactly the implementation of the said missing hardware functionality:

http://blog.plan28.org/2016/10/how-we-got-to-where-we-are.ht...