Was Half-Life controversial for casting the US military as the enemy?

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.