The physical evidence of evolution is literally in every organism that you view in your daily life. Yes, you will not see them speciate in front of your eyes because it takes hundreds, thousands, or millions of years for speciation to occur but you can see the process develop in front of your eyes as evidenced in the examples that I gave.

I'm not going to go the route of ad hominem attacks but I truly do believe if you understood biology/biochemistry/physics at a higher level you would understand what constitutes as physical evidence for evolution. The definition you give of evidence (seeing speciation occur) is only partially correct. If we saw speciation occur, then sure, that would constitute physical evidence but that's not the only type of physical evidence that exists.

For example:

There is a medical test called 16S ribosomal typing. This test is done when a doctor cannot figure out what pathogen is causing a certain pathology. After amplifying the rRNA/rDNA through PCR and examining the results they are able to compare the pathogen on an evolutionary chart to make very accurate predictions on what the organism is and how to further treat the patient. I think most would consider this very strong physical evidence for evolution (ie by looking directly at the organism and determining it's phylogeny through evolutionary genomic features we can cure disease).

On the second point. Why would God not be in control of those natural disasters? According to Christianity God created the universe and the laws observed within it. I can't see how God could not be held responsible. I am anticipating that you will counter this by saying that God just set the laws of nature in motion and therefore can't/won't alter it to protect human lives. If this is the case then we run into the very standard tri-omni dilemma in which God cannot be omnibenevolent, omniscient, and omnipotent at the same time. This dilemma also holds true for Free Will as you described in your article.