GitHub's Hubot does this too, and I don't think it's a bad idea. It's very similar to typing commands at a terminal, and has the advantages of being innately asynchronous, and telling everyone else in the team what you're doing.
Consider the security implications of arbitrary commands like he suggests, instead of using, I dunno, SSH or whatever.
If an attacker has access to Hubot, then they already have access to everything the Hubot server can do.