I’ve just encountered this behavior with WebTop, and IMO, it’s very badly broken. If the software center is going to allow us to install software in a point-and-click manner, it likewise needs to allow us to remove it, safely and completely, in a point-and-click manner. But as noted up-thread, that’s not at all what it does. When I try to remove WebTop, for example, it doesn’t (say it’s going to) remove any of the binaries, or Java, or anything like that, but it does try to remove the mail server and everything else that acts as a webmail client.
I can run yum remove nethserver-webtop5, of course. That should remove all the templating, redirects, etc., so it doesn’t interfere with the rest of my server–but it doesn’t do anything to remove the bloatware that is WebTop from my system (sorry, not very impressed with WebTop at the moment).
Software installation can’t be an irreversible process. I agree completely with @dnutan about the expected behavior–there has to be a way to make it behave as expected.