The church connection is tenuous at best. Basically, she'll be paying a whole lot more for the exact same investments that she can get at Vanguard, namely much higher expense mutual funds. The Thrivent guy/gal is a broker, pure and simple. Or as the regulators call him/her, a registered representative. He/she is a salesperson, nothing more. Any Lutheran connection is merely a way to increase sales. Just like the First Command bozos that played up their "we only help military people" which should read, "we only screw military people out of thousands of $$ by putting them into really, really high priced mutual funds and insurance."
If she wants to support her church, or the Lutheran church, she can take the money she saves by staying at Vanguard at actually give it to her church. This could be thousands of $$ per year.
You could always tell her than I'm Lutheran and only invest at Vanguard and in other really low costs mutual funds.