Rules of Engagement
Here's from a 2008 news article:
"A U.S. Border Patrol agent was injured after being struck in the head with a large rock while attempting to apprehend illegal immigrants near Douglas on Sunday.
"At about 8:45 p.m., the agent observed five individuals cross illegally into the United States near the international border fence and Bonita Avenue, according to a news release issued by the Border Patrol on Monday.
“As the agent attempted to arrest this group, a shower of rocks was thrown over the fence from Mexico at the agent. The agent was struck in the head with one of these rocks and immediately took cover to avoid further injury. The illegal immigrants were able to abscond back to Mexico,” the release stated."
This has obviously happened before (probably many times) without the use of deadly force as a response. The BP has to have trained its agents in dealing with these situations and have strict rules of engagement.
If the agent followed the rules, then he's doing his job. If not, then he has to deal with the consequences.
And as for rocks as deadly force, try some Google searches. I couldn't find any instance of someone being killed by a thrown rock (excluding dropping rocks off of overpasses onto cars). You may feel that the agent in 2008 would have been justified in shooting the rock throwers to defend himself, but he withdrew. I would assume that's part of their ROE.