Complex sentence: The main objection heard from security researchers is that malware should not be allowed on a secure operating system in the first place, and that subsequently the tool only partially cleans a small percentage of the computers the Microsoft operating system let be infected.
Split into simpler sentences: The main objection heard from security researchers is that this malware should not be allowed on a secure operating system in the first place. And that subsequently the tool only partially cleans a small percentage of the computers the Microsoft operating system let be infected.