How can I stop Entity Framework 5 migrations adding dbo. into key names?

You can customize the generated code by sub-classing the CSharpMigrationCodeGenerator class:

class MyCodeGenerator : CSharpMigrationCodeGenerator
{
    protected override void Generate(
        DropIndexOperation dropIndexOperation, IndentedTextWriter writer)
    {
        dropIndexOperation.Table = StripDbo(dropIndexOperation.Table);

        base.Generate(dropIndexOperation, writer);
    }

    // TODO: Override other Generate overloads that involve table names

    private string StripDbo(string table)
    {
        if (table.StartsWith("dbo."))
        {
            return table.Substring(4);
        }

        return table;
    }
}

Then set it in your migrations configuration class:

class Configuration : DbMigrationsConfiguration<MyContext>
{
    public Configuration()
    {
        CodeGenerator = new MyCodeGenerator();
    }
}