Any idea on how to coax it back out without scratching or gouging the finish anywhere?
Using a thumbtack I very carefully poked the seal all the way around with the side of the point and was able to lightly pry it in a corner to get the end of the pen past the seal. Everything is fine now. Everything still works.
Note to everyone, it takes almost no pressure at all to get the pen seated properly, if you push it in too far (because you have fat fingers and you can't tell how far you're going past your case, like me) it can get stuck on the seal. Lightly press the pen back in and when it clicks, it's seated, stop pushing.