Sorry, I think Isabel is established as a name in its own right to not worry about its origin.
Also, I don't get this thing for having names that 'go'. You're naming an individual, surely that should be your first priority? Obviously you'd avoid naming daft names like here are my children "Tosca" and "Josca" but beyond that, go for what name is nice. After all, your children will only spend the first 20 years of their names in your family unit - after that, they will spend the next 60 years (hopefully) in their own family units, so for 3/4 of their lives, their siblings names will be gloriously irrelevant.
Furthermore, Elizabeth is the sort of name that you can shorten quite easily, and probably will be shortened. (I know very few Elizabeths who are actually called Elizabeth). So you'll probably end up saying "This is Issy and Beth" or whatever instead.
Even if they don't go in the one mouthful, you'll soon find a way round it, like "This is my eldest Isabel, and my youngest daughter, Elizabeth". When introduced in that context, it wouldn't notice.
If you like the name, I'd say go for it!