Yes, you can file as MFJ for your Federal return.
New Jersey requires that you file as MFJ if you filed as such on your Federal return (different states have different rules).
You will be able to indicate the dates your wife lived in NJ, and also be able to either adjust your Federal income (subtractions from NJ income) to not include her Maryland income OR get credit for tax paid to Maryland.
She will need to file a Part-Year Maryland return as MFS.
Click this link for more info on Married Filing Separate States, since you did not live in MD at all.
As far as the cost to download/efile a second state, I believe it is $39.95.
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