I see a clear case for a Dependency Injection pattern.
Let's build a simple example, with Read, ReadLine and WriteLine functionalities polymorphically: your students must write a homework in which a number given in the Console.ReadLine() must be parsed as int and returned to the Console Window.
Usually a student writes something like:
class Program
{
    static void Main(string[] args)
    {
        var stringValue = Console.ReadLine();
        int number;
        if (int.TryParse(stringValue, out number))
            Console.WriteLine($"The double of {number} is {number * 2}");
        else
            Console.WriteLine($"Wrong input! '{stringValue}' is not an integer!");
        Console.Read();
    }
}
Now, instead, create an interface for the Console functionalities:
public interface IOutput
{
    void Read();
    string ReadLine();
    void WriteLine(string text);
}
A student must create a Homework class that wraps all the required homework code, using an IOutput instance in this way:
public class HomeWork
{
    private IOutput _output;
    public HomeWork(IOutput output)
    {
        _output = output;
    }
    public void Run()
    {
        _output.WriteLine("Give me an integer:");
        var stringValue = _output.ReadLine();
        int number;
        if (int.TryParse(stringValue, out number))
            _output.WriteLine($"The double of {number} is {number * 2}");
        else
            _output.WriteLine($"Wrong input! '{stringValue}' is not an integer!");
        _output.Read();
    }
}
The Main becomes:
static void Main(string[] args)
{
    var h = new HomeWork(new ConsoleOutput());
    h.Run();
}
You give them also the ConsoleOutput class:
public class ConsoleOutput : IOutput
{
    public void Read()
    {
        Console.Read();
    }
    public string ReadLine()
    {
        return Console.ReadLine();
    }
    public void WriteLine(string text)
    {
        Console.WriteLine(text);
    }
}
So the use it instead of call directly Console.Read() etc.
The student must pass to you not the entire Application, but only the Homework class.
You can create a test class that use the Homework class with some test implementations of IOutput like the followings:
public abstract class TestOutput : IOutput
{
    public TestOutput()
    {
        Outputs = new List<string>();
    }
    public void Read()
    {
        //do nothing?
    }
    public abstract string ReadLine();
    public void WriteLine(string text)
    {
        Outputs.Add(text);
    }
    public List<string> Outputs { get; set; }
}
public class TestOutputWithAValidNumber : TestOutput
{
    public TestOutputWithAValidNumber(int value)
    {
        Value = value;
    }
    public override string ReadLine()
    {
        return Value.ToString();
    }
    public int Value { get; }
}
public class TestOutputWithNotValidNumber : TestOutput
{
    public TestOutputWithNotValidNumber(string value)
    {
        Value = value;
    }
    public override string ReadLine()
    {
        return Value;
    }
    public string Value { get; }
}
The test class can be something like this:
[TestClass]
public class TestOutputClass
{
    [TestMethod]
    public void TestGoodNumber()
    {
        var testOutput = new TestOutputWithAValidNumber(1234);
        var h = new HomeWork(testOutput);
        h.Run();
        Assert.AreEqual(1234, testOutput.Value);
        Assert.AreEqual("Give me an integer:", testOutput.Outputs[0]);
        Assert.AreEqual("The double of 1234 is 2468", testOutput.Outputs[1]);
    }
    [TestMethod]
    public void TestWrongNumber()
    {
        var testOutput = new TestOutputWithNotValidNumber("foo");
        var h = new HomeWork(testOutput);
        h.Run();
        Assert.AreEqual("foo", testOutput.Value);
        Assert.AreEqual("Give me an integer:", testOutput.Outputs[0]);
        Assert.AreEqual("Wrong input! 'foo' is not an integer!", testOutput.Outputs[1]);
    }
}
If you need only to wrap the Console.Read() method, feel free to simplify all this code, but IMHO I thought that a wider view on this possible solution would have been useful anyway.