Seems to me that if the parts are being made the old fashioned way instead of CNC, that isn't quite the end of the world.
The Al Jazeera pictures of broken/crashed 737s are irrelevant. They didn't crash because of the source of airframe parts. They crashed for other operational reasons. The damage sustained was not inappropriate.
The area I might be concerned about is fatigue life if there are a lot of holes with inadequate edge clearance. The maintenance folks will know when fatigue is beginning to get into a gray area 9 times out of 10.
I have an Aero Engineering friend who is a DER and used to work for a different manufacturer of airframes. One of his primary jobs was to evaluate non-standard parts for usability or repair. I would imagine that Boeing has people in similar capacity.
Boeing has been building aircraft for quite a few years and their workforce is not inexperienced. They know how to build aircraft correctly and how to fit parts correctly if it is possible to do so without compromising the job. If they don't think that a particular part is up to the task, I would hope they have enough character and management support to say no.
I am not saying that everything is hunky-dory in Boeing land and I wouldn't be surprised if they have a closet full of rejected parts that are written off as the cost of doing business. But at the end of the day, I think that the engineers and accountants have evaluated the situation and decided that the present course is not unreasonable.