In the original Half-Life, Marine Corps units storm the Black Mesa facility a little while after the resonance cascade, with orders to kill not just the invading aliens, but any human witnesses as well. They become perhaps the primary enemies for the player throughout the middle section of the game.
Was this ever a source of controversy? Did Half-Life ever come under fire for having the player fight US military personnel and/or showing the military engaging in highly unethical actions?
In Short: No.
While it is difficult to definitively say that there were zero people in the world upset about the portrayal of the US military/HECU/Black Ops/etc in the original Half-Life game, it does not seem to be a theme picked up on by mainstream media outlets.
Searching through the archives of many, many video game reporting outlets between the announcement of Half-Life in 1997 and the release of Half-Life 2 in 2003, I have not been able to find a single occurrence of the US military beyond outlining their role in the plot during the beginning synopsis.
Also, these mentions are usually boilerplate summaries without many subjective words or emotions; the most opinionated language is usually directed at the original's platforming or level design.
In fact, the issue that seem to dominate the conversation from this time around Half-Life are Valve's decision to force customers to register their copy of the second game online with Steam.
Most, if not all mainstream negative feedback about the game during this time period is centered on one of these two issues.
In fact, before the announcement of Half-Life 2, almost, if not all mainstream game media hailed the original Half-Life as a masterpiece. If the name Half-Life was brought up in this time period with respect to any criticism at all, it is more likely to be mentioned along Doom, Quake, or Counter-Strike as a more overarching critique of violent video games as a whole.
