Cruise missiles are not magic bullets. Also, the technology required to build them isn't crazy. A clever person can build an effective cruise missile with off the shelf parts without drawing suspicion. They start to get expensive when you reduce the CEP or add things like visual recognition of targets.
If you want to destroy fixed explacements/buildings, you can build a guidance head to fit on anything with engines and control surfaces for less then $1,000. If you want to attack moving targets, you'd probably be out of luck unless you had someone who was more then clever, but cruise missiles are designed mainly for use against stationary objects, so it's not a huge loss.
The sophistication of the Tomahawk won't be matched for $1k, but you don't NEED that sophistication for a surprise attack against buildings/big targets.