How Do Muslims Deal with "Difficult" Parts of Prophet Mohammed's Life?

First, this is not meant to be an insulting or hateful question. Please prayerfully consider answering it for the sake of a true seeker soul. I have long respected and honored Islam and the Prophet Mohammed. I intend no harm. However, I have often considered becoming a Muslim, but have been held back by several things. The following is one of them that I hope to resolve. Might I add that one of my closest life long friends is a Muslim and I am close to a local Sheikh and pray often at local Masjids. There is nothing hateful meant by this inquiry. I just want to learn. There are stories of the Prophet's life that are horrendous, most of which I have no clue how to resolve their veracity. One example would be the murder of Umm Qirfa. This anti-Muslim site, here tells much of the story from what appear to be real sources from Hadith, etc. Is this story true? How can anyone justify so inhumane a murder? Thank you,