Hello again pinkkat.
In Pennsylvania, polygraph tests are not admissible in court and are useable only as an investigative aid. See this PA Attorney General's website for a discussion of polygraph tests in your state and how the process works:http://www.attorneygeneral.gov/crime.aspx?id=204
Your roommate's desires will probably not be determinative of what will happen, though sometimes an expressed desire not to prosecute will prevent the filing of charges. What is most important is whether the investigators believe they have sufficient evidence to support charges and, ultimately, a conviction.
At this point, you should not be overly apprehensive about the situation. If you did not take the money, you will likely pass the polygraph. If you do, that will probably be the end of the matter.
If the officers do submit the matter to the district attorney, it will then be up to the DA to decide whether or not to file criminal charges. At the time you meet with the officers to take the polygraph, you can ask them to advise you of their decision and then, if they refer the case to the DA, ask the DA to provide a notice to appear if charges are filed. Most will do so and, under circumstances like these, this give you a chance to retain counsel prior to your court appearance. Your attorney could then arrange for an OR ("own recognizance") release or, if necessary, the posting of bail.
Thanks again for asking your question here on JustAnswer and good luck on your polygraph test.