The downside is that the CRISPR pill kills the gut microbial community, the bacteria are called normal flora.
If the bacterial colonies are out of balance, a number of problems may result.

That's putting it lightly... the scientific community is only just beginning to understand how interwoven our microbiome is with our body, and how intimately its composition effects our health. Perhaps using CRISPR would be a good way to target a very specific sequence found in only one type of bacteria... but we better be damn sure there isn't off target cutting and effects on non desired species before this is anywhere close to feasible. CRISPR as a safe and useful technology is still a ways off, regardless of how much we wish it wasn't. Certainly a blazingly hot area of research right now.