I left the country few weeks ago while on amnesty. I didn't do anything. Just showed my passport at BKK airport. They put a departure stamp on it and nothing more. Not problem at all.
I got in contact with Samui office too but unfortunately we have a Surat Thani stamp. They told me we have to go to Surat Thani. Anyway you don't need to go there by tomorrow, that's for sure. The most comfortable way is to take the night boat from Thong Sala at 9 pm. You arrive there at 5 am. Go at the office at 8:30 when they open. It won't take long. So you can go back to the pier on time the 11:00 speedboat to PN. The only thing is the office is a long way from the pier. You need to take a tuk tuk or a cab, ask the driver to wait for you because the place is in the middle of nowhere and go back with him. A little expensive so. Anyway we can go together, if you want, and can share the cab at least.
I am exactly in your situation. I called the Surat Thani Office twice and on both occasions have been told I do not need to go there because of the visa amnesty. The thing is advisable to close this kind of stamps. I'm in Ko Pha Ngan and Surat Thani is a long way from here but I am thinking to go there anyway one of the next few days. Just to be sure. Having been told won't be a surety when you leave the country unfortunately.
I'm in Koh Pha Ngan too and have the same stamp till May 22. I got it when they came to the island at beginning of April. I called the Samui office and they told me to contact Surat Thani office because they're the ones in charge of it. I called them too and have being told the same: don't need to go because of the amnesty. As far I understand, the thing is discretional though. I do not want to get in trouble the day I will the country. Unfortunately "they told me" is not a paper or a stamp. So I'm going to Surat Thani anyway next Tuesday. I think it's safer.
Just one more question, Robert. Do you think I can go to Samui immigration office instead of Suratthani? Suratthani is much a longer way from Pha Ngan. Thanks.