I don't feel ashamed to be using java in our games, on the contrary we want to raise awareness of the benefits of java and try to remove the stigma that java has.
Success stories like minecraft will repair java image if people know they are made with java, if every developer that has some success tries to hide it nothing will ever change. There may be no obligation to do that, and you believe that it would be bad for business but showing that minecraft is made in java, that it is powered by lwjgl, etc would help the community a lot.
Also it may be the best option right now to embed a jvm with your installer but that will never help make the java runtime be on more machines. If every developer made his own embeded flash plugin without using the one installed in the browser, flash would not be installed in all those machines and they would not be in the dominant spot that they are now.
Just as an example this
is a blog post making some analysis of unity's penetration, in the post the author compares unity with flash, and at some point uses minecraft in an example, talking about the problem of having to download an exe, and how that is less friendly than having a browser plugin, never knowing that minecraft is made in java, and that it is available as an applet. This is not just a problem of a person being misinformed, but of java developers actively trying to hide the fact that they are using java.