If you was fimiliar with histology of intestine or stomach and know the characteristic features of them ,, then you can recognize any initial damage or any abnormal structure... anyway you could focus on the epithelial lining, villi length and width , percentage of goblet cell, apoptotic cells in addition to the thickness of mucosa and related structures...... crypts depth of intestine and strucyure may be good indicator
I agree with Ammar. You could recognize little damage by knowing normal histology or comparing with a normal sample you use as control.
In addition to measures and observation recommended by Ammal, you could evaluate immune cells infiltration; and if you do Alcian Blue or PAS staining (or both AB+PAS) you could evaluate different mucopolysaccharides.
Maybe the paper "A guide to histomorphological evaluation of intestinal inflammation in mouse models" could help you in knowing what and how to evaluate. It is a nice guide. https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25197329/