1. Users can be foolish or even tricked into installing apps and entering commands. If iSH provided a possible attack vector, these kinds of users would get bitten (and they would complain about weak Apple security). As Apple really does seem to be making a strong effort on security (and privacy, it appears?), losing a few useful apps and a few users is worth the trade.
2. This is a bit more of a stretch, but for various reasons Apple wants to control the macos/ios development process. Whether it's to force developers to own Mac computers (when xcode could probably run quite well on iPad Pro...), or to perhaps guarantee a more consistent outcome (which ultimately should affect the users in a positive way, or at least a less negative way), Apple wants to control the process.