No problem it's what we are here for.
There are plenty of 'non touristy' places, Iraq and Iran for starters. But remember, touristy places are touristy for a reason, if for example you visit the region and miss the Pyramids or Petra, you will kick yourself! Plus you can still head to the 'touristy' places and see them independently. Egypt is a prime example as one of the biggest tourist draws in the world, you can see a side of it that most tourists never will, and only come into contact with them at the major sites (ie the pyramids) when they get bussed in en masse and then leave with their air con coaches going back to Sharm el sheik.
Remember also that you are only planning for six months, so if you add another place to the list I gave you for example, then I recommend taking another place off.
Now, as for safety, this gets asked so so much and you really shouldn't worry. Basic common sense precautions will see you fine. Dress modestly, learn a little basic arabic, if you are unsure of custom then look at what the local women are doing. If you are not married, then wear a cheap wedding ring anyway, it may stop a few stares. That's pretty much it.
Yes there have been isolated incidents of kidnapping in Sinai, but guess what? People get kidnapped in London, New York, Ontario, Tokyo ... Thousands of people visit Sinai every single day and are perfectly safe. Again, basic common sense precautions will see you safe.
As for accomodation, you can get a good, clean hotel room (mostly with private bathrooms) pretty cheaply depending which country you are in. Spain and Turkey will probably be the most expensive. You don't need to spend more than £10 - £15 GBP a night. Obviously dorms and cheaper rooms (shared bathrooms etc) cost less.
