I am in a philosophical mood today, so feel free not to ready this post if you are not into a long answer.

I think that in order to answer this question we have to first define "stress".

So, I went and looked it up in the dictionary:

http://www.merriam-webster.com/dictionary/stress

So, like many other words we use regularly, this is a very ill defined term.

It can be positive (such as the physical stress we use to create a beautiful sculpture or even the stress we use to write on the computer).

In fact one of our problems is that we can't create enough physical stress with our muscles to do those things, because we are limited in our ability to exert such force.

If stress alters an existing equilibrium it can be beneficial if this equilibrium was not ideal or deleterious if it was.

We tend to think that something is stressful if it leads to unwanted change and not stressful if it is the change that we want. But, in reality, both are stressful. Both require a physical or chemical change, both require efforts and both create strains.

We decide if something is stressful by the end result and not by the process itself. That is why we attribute negative consequence to "stress".

Even diseases (which are unwanted changes) can be see as an adaptive response to external forces of chemical changes.
For instance: cigarette smoking puts enormous strain on the cells lining the respiratory system. Their way to respond to this and not die is by changing their structure. They stop putting their energy into creating those small hair like structures and this way they can survive the ongoing environmental stress. The cells of the delicate epithelial lining also undergo changes that make it possible for them to survive this insult. They become more resilient to environmental cues. Those initially positive changes that enable the cells to survive (and the person to continue smoking because he can't notice any discernible harm) eventually lead to inability to clear secretions, fight infections and many times also a malignant transformation of cells which have become resilient to numerous ongoing insults.

What we call a stress response is the physiological way in which our body responds in situations that require fast action.
Our body is adapted to this kind of response and it overall has a beneficial effect. We need this kind of stress. We need a good surge of adrenaline every now and then.

This kind of stress is short and always followed by relaxation and recuperation. For instance: After we run, our body rebuilds our muscles that suffered some damage from such extensive use.

But, there is also a different kind of stress which is caused by the constant exposure of our organism to what is not physiological or natural.
Cigarette smoking is one example, but there are many others.

This kind of stress is caused by fighting our nature, by suppressing our normal emotions, by ignoring our basic needs, by exposing our body to chemicals it is not accustomed to. It forces our body to constantly adapt, to constantly change, to constantly lose its equilibrium, without having time for recuperation.

It is this chronic non-physiological chemical, emotional and physical stress which is harmful.