This is well written, but I think you've been too hard on it. I think Witness is a superb film, both a personal favourite, and one of the best films of the 1980s. Weir's direction is superb. Harrison Ford has never been better, and the chemistry between him and Kelly McGillis is electrifying. I find their love story deliriously romantic and beautifully sad. As for the thriller elements, they work perfectly well, I think. But what I most love about the film is the way violence is never trivialised. One act ripples throughout the entire narrative, and in the end, evil is only defeated through pacifism and the power of community (there are so many Amish witnesses at the end, and Schaeffer is beaten because he can't shoot all of them).
Also, this film had a profound effect on me when I first saw this at the age of 12 (you can read about that in this article, if you're interested). :)