Even if you use the spider to chase Kistandalius from his shop (or use the mage's swap places special move repeatedly), he will still detect you trying to enter the back room and teleport you out. If you try to use a teleporter stone to get in, he will teleport you out before you have a chance to pick it up, causing you to loose it (though there are workarounds for that).
The only things of value there are a spell book, and a potentially powerful dagger in the chest. He sells spell books and there are lots of swords around that are better than daggers (even with Assassin's Kiss maxed), so a missed opportunity to get in is not a big deal.
You can kill Kistandalius to get into the back room, but then you can not purchase spell books, charms or jewelry from him. An area effect spell that doe not need a target (such as Poison Cloud) can be used to kill him without causing a reputation drop (cast it near but not directly on an NPC). Some NPCs are protected, and can not be killed.