It seems that this is caused to the following Eclipse issue:
"Windows 7 Libraries trigger rebuilds"
When I turned off "Refresh using native hooks or polling" (Preferences, General, Workspace) this behavior was over.
It is thus not a BusinessEvents Studio-specific issue. It is also not a m2e-related issue. Using any kind of non-trivial Maven POM makes is more visible, though.
(I think Bug 342931 is definitely worth upvoting: in my personal opinion the auto-refresh is a very happy feature of Eclipse. I've had so many times Eclipse being out of sync with the file system after using tools like TortoiseSVN to mess with my work space outside of Eclipse.)