Headscratchers / Hunt Down the Freeman

• How was the G-Man's plan supposed to work with such awful timing for its execution? Sasha is murdered just after Gordon and Alyx end up lost in space-time for a week due to the teleporter malfunctioning. By the time they get back to City 17 over a week later, the rebellion has started in earnest without them, the Citadel is under siege, the Combine has way more problems to deal with than Mitchell, and Breen likely wouldn't be remotely interested in giving Boris resources when the rebellion is right at his doorstep and causing mass destruction, meaning the effect of making Mitchell a long-term target is ineffectual at best.
• If the POTUS surrendered humanity to the Combine, what was there left for Dr. Breen to do?