This is a sidebar comment to open, but just to be clear, CR does not demonstrate intelligent design, but does demonstrate the limits of the natural processes. But maybe you get that, and just worded this too succinctly.
Your main point is extremely important! I think there are two approaches, the first is a brief scientific one, and the second theological.
Scientifically, there are vastly more bacteria and viruses that are an utterly essential part of the ecosystem than those that cause us harm. AJ Roberts has good discussions on this, for example https://www.reasons.org/explore/blogs/theorems-theology/read/theorems-theology/2017/12/14/viruses-mosquitoes-and-suffering-bad-or-good In some cases diseases are just bacteria out of place, like gut flora getting into the abdominal cavity – very bad. But we humans absolutely require the microbiome that lives symbiotically within us. There are only a tiny tiny fraction that cause disease and suffering in humans.
Turning to the theology, there is still a question about those few that cause so much suffering. I’m with you on struggling with it. Behe mentions in passing that his argument raises these questions about falciparum (malaria) itself, but says that’s a discussion for another time.
For myself, I start with Jesus. If not for him, I would not know what kind of deity this is. But since he has revealed his heart to us in Jesus, I can say “There are things I do not like and I do not understand, but other things I do know let me trust you.”
We may one day find out many of these had or have a good purpose in the story of life. I think we run the risk, since we don’t know their purpose, of using “BadGod-of-the-gaps” thinking. In other words, because I don’t like it and some diety made it, the deity is evil. Some of this is clearly beyond our pay grade.
I’ll add a couple of personal thoughts. For me, recognizing that there are a handful of uncomfortable possible implications in places does not trip me up from being able to honor God for the incredible beauty and complexity of all he has done. Touching biology at this level is like trying to touch infinity or eternity - the complexity of the molecular biology utterly boggles the mind. I know a couple of college students studying biochem, and they are slack-jawed at it all, and wonder how anyone can think the biomolecules figured this all out on their own. So I think it’s right to be grateful for the gift of life in all its splendor, while acknowledging the pot holes on my road. I can’t fix the potholes, but I have good reason to drive around them and keep moving forward. And I can’t stop others from focusing on the potholes and missing the glorious views.
Hmmmm, posed as darkly as possible, cuz perhaps that’s the way aggressive atheists most likely would ask it? But for that particular question, I personally think God is done creating (we’re in the seventh day).
Hope that all helps!