This whole thing is way deeper than some lowly un ambassador.
Maybe the ambassador discovered direct links from the Administration to the MB in North Africa, (in fact, the whole "Arab Spring") of arms trafficking, money transfers, etc. Supposedly, he was investigating such.
Somewhere, there may be some very valuable information if it hasn't been sequestered and/or destroyed, but the message has been sent, even relatively high profile people can be murdered in plain sight.