It would be a very easy change for us to limit the Harvest Depot withdrawals to Trustees only and make it so that the permission level on the amenity only affects who can craft from it. Would this be a better solution than what we have now or would it cause more problems?
When it comes down to it, just adding logging isn't going to fix your problem. An unscrupulous person could still join your guild, remove all the items and leave. The log would just tell you who did it, which you'd probably already know anyway. We'd have to implement limits by rank and now you're talking about a lot of work for just a single item in the game. I don't think we want to start down the road of managing everyone's social interactions and create the expectation that every new feature we create must have this level of administrative features.
I'd still like to revamp the access level system for housing so it can be more specific, like guild rank permissions, but that will be further down the road. In the meantime, if limiting withdrawals to trustees will be an improvement over the current situation, I'll make that change.