It seems to be impossible to prevent application from reloading on a class file change when "Serve modules without publishing" is enabled. I have "Never publish automatically" selected in Server configuration, but every time I modify a class file (not a JSP - with JSP changes all is OK), my web app gets restarted.
After some digging around I found that changing <Context .. reloadable="true" to false in server.xml stops the reloading.
But how do I tell WTP to publish applications with reloadable set to false? It seems to be always publishing with reloadable="true", regardless of my publishing preferences...
Going to answer my own question. Just go to the Servers view, double-click on the server, select Modules tab at the bottom, and disable auto-reloading there. Done.