As a women who has had epilepsy for over 20 years, I know that it is very possible for women with epilepsy to have children safely. There are some medicines that are very dangerous for the baby, but there are others, such as Lamictal, that are relatively safe. I recommend talking to her neurologist. Express your desire to have children and your concerns about the medication. Ask if there is something in her medical treatment that can be altered to use medicines that are safer for childbearing. Granted, this is a tricky time when a person is first diagnosed. That said, there are multiple options that you can discuss with her doctor - and with the medicine options today, it certainly is possible to have a healthy pregnancy with epilepsy.
Regarding the partial seizures happening at the wrong time - are they fairly controlled? Even women with grand mal seizures can conceive and deliver children safely. Again - her doctor can help with understanding this.
Most importantly, pray and ask God for guidance!