How can I get my wife to stop nagging about a few murders?

This thread suggests that what you need is to get in-game time to pass and to advance the story further, if you can. (There is a mention of 8 in-game days, but no source to support it.) It may also help to do good deeds along the way. You should be able to measure success in the same way you've noted a lack of success so far: as story time and in-game time passes, people should be referring to you as less of a jerk (and murderer) and more of a nice guy as far as murderers go. Eventually, your crime spree will be a thing of the past.

To make this less of a problem in the future, you might consider killing people in front of a smaller audience ... perhaps an audience of none? Dead NPCs, as they say, tell no tales.

Honestly, the only definite solution is to kill her. Both me and players I'm friends with have fallen into this irritating trap. While I'm open to the possibility that everyone will eventually shut up about me being a murderer, I haven't found any evidence that it will ever happen. Everyone I've talked to hasn't had any luck.

If you're less of a cynic than me and want to give it a shot, try doing a bunch of good deeds. Spend time going around town and impressing people. Don't kill anyone else.

I think over time most towns people will forgive/forget but it might take a lot of bribing for you wife. When in doubt take her on a long journey through balverine infested woods.