I haven't found an easy way to do this, and I hope someone else can improve on my answer. Here's my approach, which requires some familiarity with HTML. First, publish each function separately. You need to set evalCode to false, which you can do using the menu File -> Publish configuration for myfunction.m or these commands:
publishOptions.evalCode = false;
publish('myfunction.m',publishOptions)
Then you cut and paste the relevant HTML, which will be a block like this
<pre class="codeinput"> ... </pre>
into your main published file.
(Edited for clarity.)
