The following information is located in Game Update 1.3 patch notes which may be of interest to you regarding this topic:
Simple fix idea since you guys couldn't fix it your way. Remove all the trash from between the bosses for guilds that have cleared 4/4 at least 3 times already. Then we can switch instances all day long with no worries. 8P
I joke, I kid. In all seriousness, why would there be a switching of instances in the first place. Have a set cap in multiples of 8, and don't switch instances. So an instance could be 64 player cap perse before a new instance is opened up. Any combination of 8/16 man groups make up this cap but here is the rub. It is a dynamic set that if 56 people are already in the instance and a 16 man group wants in, they will create a new instance. If an 8 man wants in, they get into that one.
Make the instances have a timeout factor of 5 mins as well. That "slot" is held for 5 mins. This allows for wipe recovery where people are repairing outside the instance, that way their spot isn't taken by some other guild going in.
In theory, this shouldn't be too hard to implement.