When using a siege engine in multiplayer, its possible for a non-allied player to sneak up and pack up the siege engines (ballistae, rams etc) that a player is currently sat on and operating, and just run off with it.

This is an exploitative cheat.

Can we somehow make siege engines unpackable if a non-allied or enemy player or npc is currently using it?

Yeah, this is quite dumb. especially if it was a really expensive siege engine, or is a battering ram that is mostly unarmed. My best suggestion for now is to have a large soldier escort or another player protecting you.