Why not extract the parsing logic into a separate class and unit test, which is separate from your main ()?
The parsing class should receive string parameters. Therefore, you can test as many scripts as you need in different tests, without having to run the program executable, just by calling the class instead.
UPDATE
Now, if you do not want to create an additional class (I would probably still do this, just for clarity, but somehow), keep in mind that you can just call your static Main(string[] args) method from your unit test, passing various parameters to cover various scenarios.
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