Given all the circumstances you described, I think you handled it just fine. Nothing makes you think about your choices in life more than seeing the business end of a .45 from a few feet away. Yeah, I suppose you could have held them for the cops, but that has risks, too. There were two of them, and if they were really bad hombres who wouldn't want to have an encounter with the cops, they might have done something desperate, like run inside your house and take hostages. And, once they got out of there, I think the *last* thing they would have done is call the cops on you for brandishing.
I doubt they'll be back. Now, since you're on the road a lot, what means does your wife have to handle a similar situation? What's the home security situation afa hardened doors and windows, alarms, etc.
K