Last night I ran Assault on the Kingdom of the Impossible. It went fairly well, but the last encounter gave me some trouble. For those who aren't familiar with the scenario, the players have the option of convincing the boss (a druid) to turn himself in to the Society rather than fighting. Though they succeeded in winning him over, the fighter in the group (whose alignment was NG as I recall) insisted on killing the boss's animal companion anyway. I thought this was pointless and potentially evil since the boss had already surrendered, so I talked him out of it.
Another problem arose when the lone Qadira faction member had to work out a deal with the boss. The notes for this faction mission say that the player must give a good roleplaying reason for the boss to comply, but the player simply threatened to kill him. I again objected for similar reasons. He relented and went for a more diplomatic approach.
I'm still a fairly new GM, so I want to ask if I handled the situation appropriately. Was I railroading too much by not letting the players do as they please? Should I have just started the fight and made the party face the consequences? If I had let the fighter kill the animal companion, would that warrant an alignment infraction? The players all seemed happy when I ended the scenario and handed out chronicle sheets, but I don't feel too good about my actions as a GM.