They have the same intentions and so there is no contradiction
The Red Queen was programmed to value human life and so it was the act of rebooting humanity that she has a problem with. The murdering of all those people is the conflict, not the saving of humanity.
The Red Queen: When this recording was uploaded to my data stream, it created a conflict in my programming. I was created to serve the Umbrella Corporation, but I was also programmed to value human life. Dr. Isaacs allowed the virus to escape. He murdered over 7 billion people. My programming will not allow me to harm an employee of the Umbrella Corporation. I am powerless to stop Dr. Isaacs, but you are not.
Resident Evil: The Final Chapter
Dr. Isaacs himself also wants to save humanity, however, he believes the way to do this is to kill off most of it and start again with a base population (cough Thanos cough). This population is namely the rich and powerful who are to rebuild humanity once the remnants of the virus have been cleared from the world and start over again.
Dr Isaacs: We're here today, not just to talk about the future of this company. We're here to talk about its destiny. We're here to talk about the end of the world. We stand on the brink of Armageddon. Diseases for which we have no cure. Fundamentalist states who call for our destruction. Nuclear powers over which we have no control. And even if we navigate these dangerous waters, we face harder, even more inevitable threats. Global warming will melt the polar ice caps within 80 years, flooding 90% of all habitable areas on Earth. Unchecked population growth will overtake food production in less than 50 years leading to famine. And war. This is not conjecture. This is a fact. One way or another, our world is coming to an end. The question is, will we end with it?
Alicia: What do you propose?
Dr Isaacs: I propose that we end the world... But on our terms. An orchestrated apocalypse. One that would cleanse the world of its' population but leave its infrastracture and resources intact. It's been done once before. With great success. The chosen few will ride out the storm, not in an ark as in the book of Genesis, but in safety. Underground. And when it's over, We will emerge onto a cleansed Earth. One we can then reboot. In our image.
Male board member: And just how do you intend to achieve this?
Dr Isaacs: The means of our salvation are already at hand. I give to you, the T-virus.
I believe that Isaacs just saw the only way forward as rebooting humanity and so would have believed that his creation, The Red Queen, would also see that as the only option. He created her to have his same ideals but being an intelligent AI she came to her own conclusions as to how that should be done.