I'm not sure about any names beginning with an A as then she'll be A. Cook or Cook A. (which sounds a bit too much like cooker for my liking). Personally, I also think names beginning with I, E or Y are ruled out unless you don't mind the nn "cookie"... which she may end up with anyway given the surname but you may not want to guarantee it which you will with Cook Y. or Cook E. or Cook I.
Ailsa and Alice Cook both sound lovely, and I think the initial thing isn't such a big deal really. I think Cook is such a straightforward name a lot of things will go nicely with it actually, it would balance out longer names very well.
What about Penelope? You could nickname Penny.
I have to say though, I think Flora, whilst a nice name would also be a mistake with the margarine association in this instance!