First of all, mazal tov, or be-sha’ah tovah, as the case may be. Many blessings to you for a healthy child and much joy.
However, these customs address Hebrew names, and you are asking about the English name. Presumably you will give Isabelle a different Hebrew name than Bella has. Then, Jewishly speaking, grandmother and granddaughter will not have the same name at all. You might also consider, in the interest of appeasing your maother, making “Isabelle” your daughter’s middle name. (Tou can still call her Ellie, of course!)
Ultimately, however, if these accommodations do not comfort your mother, you will need to make your decision based on how you value your relationship with her. Given that much that is distinctive about Ashkenazi naming customs is based on (non-rational, beyond-the-law) superstition, and that it is often very difficult to talk a superstitious person out of being so, you may find no way to convince your mother to feel good about having a granddaughter named Isabelle. If that is the case, Jewish tradition presents us with a whole host of values (e.g., honoring father and mother, shalom bayit/peaceful home) to suggest that, while you may technically be in the right, it might also be right to defer to your mother’s wishes.
On the other hand, if resentment toward your mother, should you not give your daughter the name you prefer, would cause enough damage to your relationship as to outweigh any damage that would result should you follow your preference (thereby endangering the peace of your home and your ability to honor your mother in other ways), you are faced with a true spiritual dilemma that only you can resolve. I recommend prayer, reflection, and compassion for everyone involved.
I wish you peace and a happy solution to your dilemma.