Distra,
I have both, a Witness 45 and the CZ-97B. Even thought they are based on the same design, they are distinctly different. The Witness is a 45 with essentially the same external physical ergonomics as the CZ-75, a great feature, and it still holds 10 rounds in the mag.
The Witness will typically have a better SA trigger out of the box, but I don't like the DA; the short hammer mainspring makes if difficult to have a light DA, although it can be achieved, but who shoots in DA much anyway?
The CZ is significantly larger externally compared to the Witness. The Witness is a better "feeder" with most bullet types including JHP's. My Witness would not feed 200 LSWC reloads. There is a sharp ridge on the mouth of the chamber I had to smooth out, after that, it fed the 200 LSWC's without a hitch.
Accuracy is toss up, both are excellent out of the box. The sights on the CZ are much easier to upgrade, the Witness front sight cannot be replaced without having the slide machined, and I'm not a fan of the standard Witness front sight, although the LPA rear sight is great. The Wonder finish on my Witness is uneven and blotchy, but it's not a high dollar gun. The CZ finish can be uneven from time to time as well.
The standard Witness mag on mine was not very good, had to replace it with a Mec-Gar for reliable function. EAA customer service has the worst reputation in the industry and deservedly so; CZ's is much better.
As you mentioned, the Witness is cheaper and represents a fanstatic bargain for what you get. I prefer the CZ, but I have tricked mine out and I have medium+ hands, so the 97 fits me better.