If you chose Married but withhold at the higher single rate (there is not an option for Married Filing Separately on the W4), this will not affect your actual tax return filing status. The W4 is simply a form your employer uses to determine how much to withhold from your paychecks.
You can still file Married Filing Jointly. Since MFJ generally provides more tax breaks and a better refund you could possibly see a larger refund since your employers would have withheld your federal taxes at the higher single rate.
Here is a link to more information on Married Filing Joint versus Separate
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