The easiest way I've found is to enclose the chunk in 4 backticks, so this:
````
**my Rmarkdown doc**
Here's a chunk:
```{r chunky_chunk}
getwd()
```
````
Becomes this:
**my Rmarkdown doc**
Here's a chunk:
```{r chunky_chunk}
getwd()
```
That way, you can still use code formatting. The other option is to indent everything by 4 spaces (like on Stack Overflow), but the lack of a button to do that makes it more annoying. Also, you'll see that the parser doesn't handle unbalanced quotes, like the ones that tend to show up in contractions.
I feel like this should be a sticky in the #shiny and #R-Markdown categories. We get some scary looking posts there.