Oh boy. Clerks, clerks, clerks. You're clearly in the right calling by your attention to detail, but there's a spirit of the law you need to also observe...
All the recommendations above, except for one, do more harm than good ... the acceptable solutions are that you either tell them to get over it (incidentally, not acceptable), or get her baptized (incidentally, a *bad* reason to get baptized)? In many cases the mere suggestion is more likely to end up with a DECREASE in people getting baptized due to them taking a very justifiable offense. I mean the worst thing you can tell them is that their marriage is so unimportant that 6 years after this glitch was brought up here (this thread was started 6 years ago) the program still seems to suggest that their marriage doesn't count. Explaining to them "why" will not make it better.
There are better ways of dealing with this problem, and it starts with valuing the person above the value of the record. One should consider that these aren't the 1800's ... there are tons of records showing every person's maiden name in the 2000's.
And if you play your cards right with the part-member family (ie. that means you value their membership ABOVE perfection in this part of the record - a record which, by the way, is routinely wrong for many families in every single ward for all kinds of reasons, and many, maybe most, never get fixed, and yet the church is still true) ... if you value their membership and do the right thing BY THEM by putting their needs first, then there will probably be children of that family that will be rooted in the gospel as they mature and raise children and grandchildren in the gospel ... a child or grandchild will fix it when that parent dies. They will. But they won't be there to do that if you value the perfection of their particular record more than the membership of the people who's record that represents. Bah, who cares, you got the record right and that's what counts. Right? No. The Lord cares more about the individual.
When dealing with such matters let's not put the cart in front of the horse. People matter more than records. Baptism and fellowship is more important than getting a maiden name record perfect ... especially when you're working on raising a generation that will stay in the church and fix obvious errors when they see it in a genealogical record some day in the far future. As for myself I've made myself to fix it when the spouse gets baptized ... which I'm feeling confident because we're doing right BY HER.