When you say "we", do you also mean that she is the primary (not secondary) cardholder for the Sapphire and Ink Bold card? Chase does seem to limit the amount of cards you get in a short period of time. I was able to get 2 cards this year and 5 months later was trying to get a third but was denied unless I cancelled one of my existing cards. Did she apply for any other Chase cards recently besides the SW RR Personal?
Just be prepared to any questions they may have on the business (how long, income, etc.). Other than that, I would tell them that you will be flying with Southwest a lot (which is true) and want to get the business credit card to separate your expenses.