Today while playing IRONMAN, I wandered into a Harpy fight. We were buffed with magic circle and our Bard activated Countersong. Neither of these worked against the Harpies' fascination. Normally, protection from evil blocks this effect and magic circle is an area version. Pweath investigate! Thankee!
IIRC, magic circle is bugged in that it does not provide the mental protection that the 1st level spells provide. I think I read that it was hard-coded as such - because it has been looked into in the past. I've previously had mixed results with Countersong and I can't quite remember how effective it was or if it worked to remove the charm. The past few runs I left some party sentry in the hall to guard for the ghouls and usually that distance is safe from the harpy effect. But I seem to recall that party members do shrug off the charm at different times, which may or may not be due to countersong?
Protection from alignment is also bugged in that it doesn't suppress ongoing mental effects like it should. (It only prevents them.) Thus, magical fear can't be suppressed this way though it should be able to.
Fixing that would be a lot of work, I think. Essentially every relevant effect would need to be modified to check for the conditions that suppress them. Same for antimagic field. It'd be interesting to have, but probably way too much work to be worth it.
I assumed that if the code can check for [Mind-Affecting] effects and block them when they're cast, the code can also fairly easily suppress them if active for the spell's duration.