How does one impeach a president for using one of his constitutional powers i.e. that of pardon?
Since the impeachment of a sitting president is essentially a political proceeding (rather than a legal one), he can be impeached for any reason whatsoever. There is nothing in the U.S. Constitution that would prevent the House from issuing articles of impeachment against a president just because they didn't like the color of his hair.
The reality of the FALN case is this: if a president who grants clemency to people who were involved in 130 bombing attacks in the United States is not guilty of treason, then nobody is under any obligation to obey any laws in this country anymore.