Yes, it does seem reasonable that you're not a "Mrs." if the names are different. Unfortunately, there aren't too many alternatives. My wife is a Phd, so she can be "Dr." but she sure isn't a "Mrs." because neither last name would make sense. I don't particularly care for any of those titles anyway (just never seems right when I hear "Mr. Mark Kauffman") Sooooo..... personally, I like dropping the titles and just using Jane Doe + John Smith so I vote for that option because we've become so much more a casual society (unfortunately, Ms. just hasn't become too popular.)

Good luck! And good luck with kids! We hyphenated our kid's names, but golly gee; it sure has been awkward. My favorite solution (that a couple of my customers have done) is to adopt a whole new name for your new family for everyone to use.