I fired a mana burst directly at the portal as shown in the screenshot and the portal did not extinguish.

Screenshot:
http://imgur.com/a/dzNF4
Log:
http://paste.ee/p/OYpgm

If it doesn't work on the inside edge then it's probably just a missing feature/oversight in the implementation

the teleportation code runs before the impact code so I don't think this is possible.

Maybe try aiming it at the edge of the frame next to the portal block

I've tried a bunch of variant aimings. Including some that point at the inside edge of the portal frame. None of them have any effect. If you have a more specific suggestion or a screenshot of something that works for you I'd be happy to try it myself.

Screenshot:
http://imgur.com/a/0zfJ8