You can file a 90 day report from two weeks BEFORE the due date until 1 week after the due date without a fine. So the fact that Immigrations was closed on your due date cuts no ice to them as you had a 3 week window to file.
Once you're more than 7 days late you do get a 2000baht failure to file fine when you do your next report. Good news is that fine doesn't increase whether you're 8 days late or 8 months late, it's just 2000baht.
Now as far as could you have filed at an office other than where your primary residence is, that's between you and the office you were trying to file at. They don't have to let you file, BUT they can if you prove you're registered as staying there (TM30 from the hotel) to show you are at an address served by them.
Live and learn, you have 3 weeks to do the 90 day reporting in person.
I am doubtful your old passport has a Non-B VISA in it and it's far more likely if you looked at the stamp it would say "extension of stay permitted until" and have a date..
If you do have the stamp I mentioned you need to go to the immigration office <- the one that issued the extension with BOTH passports and get the extension stamp moved to the new one, THEN you can buy a re-entry permit and leave.
Sadly if you got the extension stamp FROM the Koh Samui immigration office the fact that you would like to avoid going back there doesn't factor into it ๐ You move stamps at the office that issued it