Program.cs

using System;
using System.IO;
using System.Linq;
using System.Reflection;
using Microsoft.CodeAnalysis;
using Microsoft.CodeAnalysis.CSharp;
using Microsoft.CodeAnalysis.Text;

class Program
{
    static void Main()
    {
        string text = @"
using System;
using System.Collections.Generic;
Console.WriteLine(""I only need to use System"");";

        SyntaxTree syntaxTree = CSharpSyntaxTree.ParseText(text, new CSharpParseOptions(kind: SourceCodeKind.Script));
        var coreDir = Path.GetDirectoryName(typeof(object).GetTypeInfo().Assembly.Location);
        var mscorlib = MetadataReference.CreateFromFile(Path.Combine(coreDir, "mscorlib.dll"));
        var options = new CSharpCompilationOptions(OutputKind.DynamicallyLinkedLibrary);
        var compilation = CSharpCompilation.Create("MyAssembly")
            .AddSyntaxTrees(syntaxTree)
            .AddReferences(mscorlib)
            .WithOptions(options);

        var tree = compilation.SyntaxTrees.Single();
        var root = tree.GetRoot();

        var unusedImportNodes = compilation.GetDiagnostics()
            .Where(d => d.Id == "CS8019")
            .Where(d => d.Location?.SourceTree == tree)
            .Select(d => root.FindNode(d.Location.SourceSpan))
            .ToList();
        var newRoot = root.RemoveNodes(unusedImportNodes, SyntaxRemoveOptions.KeepNoTrivia);

        var newCompilation0 = compilation.ReplaceSyntaxTree(tree, SyntaxFactory.SyntaxTree(newRoot));
        var newCompilation1 = compilation.ReplaceSyntaxTree(tree, SyntaxFactory.SyntaxTree(newRoot, tree.Options));
        var newCompilation2 = compilation.ReplaceSyntaxTree(tree, tree.WithRootAndOptions(newRoot, tree.Options));
        var newCompilation3 = compilation.ReplaceSyntaxTree(tree, tree.WithChangedText(SourceText.From(newRoot.ToFullString())));

        WriteKind(newCompilation0); // Regular
        WriteKind(newCompilation1); // Script
        WriteKind(newCompilation2); // Script
        WriteKind(newCompilation3); // Script

        void WriteKind(Compilation c) => Console.WriteLine(c.SyntaxTrees.Single().Options.Kind);
    }
}