Let's say that the boys had followed Ruby's plan for demon death. So. Every human but Nancy survives, including whatever possessed people were still healthy. Ruby is dead. The boys reconcile with Henrickson, they all leave. What happens?
Lilith drops by anyway and kills everyone at the station. And now the boys have the blood of an innocent woman on their hands and their only demonic ally is dead, and therefore not able to give them the antiLilith wards.
So, in point of fact, following Dean's plan had a better result - they don't have that particular blood guilt *plus* Ruby's still around. Dean's plan worked perfectly.
So why is Ruby upset? Because Dean can think beyond killing someone?