Before we get too carried away with protecting all animals from harm think about the last friendly (female) mosquito or black fly which you encountered. Personally, some living creatures are best when they don’t interact with us. IMHO
You missed the whole point of the quote, then.
Certainly, St. Francis would not disqualify man from defending himself from wild animals. His point, although made some 700 years old, really has less to do with animals than it does other people. It is a cautionary suggestion that those who have a penchant for inflicting wanton and unnecessary cruelty on animals will generally have no moral proscription against doing so to their fellow man. Like it or not, this has been born out in any number of studies of serial offenders, a significant percentage of whom have all indulged in animal torture.
Just as you say, "Personally, some living creatures are best when they don’t interact with us. IMHO." Some of these living creatures are other people. St. Francis was not defending the mosquitoes and the black flies, so much as he was warning us about the Dahmers, the Berkowitz's, the DeSalvos and the Klebolds.