Maybe pain can also be for the good of others or maybe it was designed as a negative experience that encourages humans to lean on God in our mechanic wish to avoid pain and suffering.
Only humans seems to see pain as a negative thing because it generally comes with emotions such as mourning, grief ect we would like to avoid.
It seems to me that you're arguing with the fantastic premise that animals are void of malice thus should not experience what is appreciated as a negative experience from a purely human perspective.

I don't know what's so problematic with bugs, plants or even hyenas exprience today outside of human malevolence of course but as you said they are all innocent therefore the short suffering of some animals is also a pleasant and enjoyable experience for their predators who would like to have a good meal.
A Christian could also argue that pain is a reminder that there could be a possiblity of a different world where none of that exist. Basically heaven.

Creating the conditions for pain isn't immoral in itself. Some cure could cause pain but it doesnt mean it is immoral since it has a good purpose.