No, you cannot put control codes into an INI unless you manually do so. However, you can convert them to something else, then convert them back later.

For example, if you know that your INI will never use ~, you can replace the Ctrl-K with ~ when writing the INI and replace the ~ with ctrl-k when reading the INI.

If you wanted to be more careful about what character is used, then write a group of characters in place of Ctrl-K... rather than just ~, you might use ^&@ or something.