I kind of just scrolled to the bottom so I have no idea if someone’s already answered this.
The Combine fought in the 7-hour war were likely an invasion force a la the United States in the actual war of the second Gulf War. The actual fighting between soldiers was over fast and with great efficiency - the force that you fight in-game is just an occupation force, like the US trying to stabilize Iraq after Saddam’s army was defeated; still a part of the universe-devouring military force, but a completely different and much more sedentary beast than the initial force that took it over.
Of course I’m using the second gulf war as a crude metaphor, the combine are technologically superior, have vastly more resources, and had several different enslaved alien species to serve as soldiers. So yeah - 7-hours is relatively long if you think of it with those odds.
*EDIT: I also think it justifies why they would have issues with capturing/killing a lone scientist and an ill-equipped resistance movement. I’d think any modern military could tell you that it’s much easier to steamroll your enemies than try to accurately and precisely remove embedded potential threats.