For some reason nothing in doc mitchell's house is marked as stealing.
Games like this have a lot of stuff for you to grab in the starting area. In fallout 3, you were free to loot the vault as you go along escaping from it, ending up with decent starting armor and weapons at the end.
If we go the "oblivion with guns route", Oblivion gives you access to a bunch of gear in the starting sewers.
In morrowind, the customs house you start in has rooms with lots of easily steal-able equipment and goods.
So doc mitchell's house is a treasure trove of free stuff on purpose- they want you to use it in your initial forays into the wasteland. They don't expect you to turn around and sell it to him, they expect you to go out and use it all.
At any rate, the only way to have him not buy the stuff would be to mark it as stolen, which would defeat the purpose of "oh yeah, take it all!"