No, you will not need to file separately. Both of you are full-time Maryland residents. Even though she was physically present in NJ, she is not considered a resident of New Jersey because she was a student, which is considered a temporary absence from her true residency, Maryland. The fact that she had no income during that stretch makes your filing much easier: Married Filing Joint on a full-year Maryland resident return. You will not need to file for NJ at all if she had no income there.
Go back to the Personal Information screen regarding your wife and state that she did not live in another state other than Maryland. Then you should be able to file Married Filing Joint for Maryland without difficulty.
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