They could include a mechanic to discard the warmachine after a quest card is completed. If you go on, you abandon your trebuchets (or whatever…) to travel faster.
That could make sense. If you're using your attack to quest, then they could make siege engines an ally that gives something like -4 willpower to the group while in play, which wouldn't affect a siege-quest but would make them pretty stupid to include in something like Hunt for Gollum or whatever. Then the quest card, when completed, discards all siege engines from play like you say.
Or maybe you cannot travel to locations while a siege engine is in play, so having one would be detrimental to the party in a location-heavy quest.
I suppose it could just as easily enter the game as a trebuchet on the walls of the white city, as Rich says, which are locations from the encounter deck that benefit the group when drawn - for example, the location could deal one damage to every enemy in the staging area if you have a suitable ally in play who can operate them, then discard the location from play. Or deals one damage at the beginning of the round while that ally remains in play (which could then lead to specialised enemies who target allies or whatever). Or something. That way, the actual war machine remains quest-specific but we still get an ally we can use in other quests if need be.
On a tangent, I think friendly encounter cards could be an interesting thing to develop. We have a small number like the Dwarrowdelf objectives, or some locations like that glade in RtM that lowers threat or whatever, but it seems we rarely get rewarded for completing certain parts of quests.