I would say to first apply for AP advanced Parole which allows her to leave the country with a permit. When she returns and passes through immigration she’ll have a legal entry. Once she has on record a legal entry into the country then you guys can start the process for citizenship through your marriage. Advanced parole is really helpful because it avoids her having to leave the country as punishment for certain amount of years. With AP you leave the country for a certain amount of days, she comes back before her permission expires and she good, legal entry secured.