I think it registers as creepy because the narrator is anthropomorphizing while we watch.

Although I agree that in the abstract I'm not bothered by it. I mean, we also kill mice in large numbers for science...

I did feel a little sorry for the ants, but it's not as if they're endangered, or have any higher-level brain functions.

I think they generally only do this to abandoned colonies.

The farmer that discovered the colony on his farm killed the infestation before the concrete was poured. They were doomed anyway.

Gooooo useless science!