What would a general discharge entail? It doesn't sound too negative.
A General discharge can be for a variety of reasons. Not enough observed service time, or lack of enough years of service time (usually less than 18 months, which Kerry exceeded, so he doesn't qualify under that standard).
Usually, a general is awarded because the servicemember's behavior while on active duty just wasn't up to the standard that would be considered "honorable". For enlisted Navy personnel, 2 or more non-judicial punishment proceedings in a 3 or 4 year period, and a recommendation for a General discharge by that member's Commanding Officer is enough.
For an officer, even 1 NJP could be enough, as the standard for honorable service has to be neccessarily higher. This could explain why there has never been a full and complete release of all of LT(jg) Kerry's officer fitness reports (FITREPs), as an NJP proceeding would have been required to be annotated on his FITREP upon the date of required FITREP submission (for LTjgs, commonly twice a year) or upon transfer to a new command or release from active duty.
If that's the line of thinking here, it would've had to have been for his already-documented failure to follow what was conceded to be a lawful order by his superiors to destroy an enemy-held encampment. This could've occasioned discipline, but I think that the Swift Boat Vets would have already blown the coverup off of that one by now, some of them most likely having been "in country" during the incident, and a defineable paper trail having to have been detailed.