There is only 1 issue I see with this. Everyone that uses the "Still learning encounter" check box would need to make sure anytimes they attempted a boss and manually took the snapshot would need to ensure they had them checked. If not they might show up as a kill and skew the count or invalidate the Killed status.
I've been giving some thought to the best way to automatically implement this, and the concern you raise here is the biggest one I have as well.
I'm considering adding another checkbox for "Boss Killed" or something to that effect, in that off-chance that a particular raid snapshot might be awarded that isn't a "Learning Encounter" but isn't a kill either:
For example, say you regularly kill Broodlord Lashlayer, but due to lag problems, you are unable to successfully pass the suppression room, or are just unable to get heals off sufficiently fast after his mortal strikes. That wouldn't necessarily be a "Learning Encounter" but it also won't be a kill, yet for your guilds participation and dedication, you wish to award points.
While generally "Learning" would mean the opposite of "Kill," there're still those potential exceptions and they need to be considered.
Hadn't thought of this one... but... well... yeah..