Good for you. Like I said earlier, there is no way to avoid conflict.
I think this thought "Don't rock the boat and make her mad, you will drive her away, and make her file for D!" is very natural. But, it is not accurate. It is important to set legitimate boundaries. The truth is that these boundaries reduce conflict and if consistent will improve the relationship.
The biggest issue I see is that this was an emotional response to the conflict with your children, rather than a deliberate boundary that you rationally set. It also blindsided your wife.
It would have been better if you could have sat down with her calmly before she went to Denver and explained that it is unreasonable to ask you to sleep in a different room. That when she returns, you are going to start sleeping in the master bedroom. That, she needs to decide what her sleeping arrangements are going to be when she gets home.
The key to setting boundaries is making sure that they are reasonable, that you are consistent, and that they are done solely to support your personal needs.
There is a tendency to use conflict like this to control and manipulate your spouse. That will just create more conflict and drive her away.
