Generally, from past experiences in different guilds, the guild chests/banks usually contained items, which consisted of profession materials, weapons and armor of lower value (useful for lower level alts), misc items that people don't necessarily want anymore, food, potions, etc. There were never any epic or high level items that people left in the bank.
It was probably meant to have it this way to prevent the problem you are mentioning. For your guild, I suggest only having items that you do not mind having potentially being "stolen." Hopefully you will never come across this problem since you will have members who you trust and will be honest in their donations and withdraws.
This is just what I've seen from my experiences, others might have a different take on this. Hope this is somewhat helpful to you.