My e-filing was rejected as they did not recognized my wife's recent change of name. I corrected the return by giving her maiden name-married name. Will that work?

That should work. The IRS checks names and social security numbers against the social security database, so if she hasn't changed her name with social security, she will need to file with her maiden name. 

You can look into changing her name here: 

https://faq.ssa.gov/en-us/Topic/article/KA-01981