Except for the fact that users are discouraged from installing from outside the repos. If they do, they are on their own when it comes time for support here in these forums, since no one here will know what changes have been made to their installation.
Like I said, it's really a shame.
I wonder how can we protect our PCLinuxOS installation? because I already installed java applications directly from the executables, like MindOnTrack, and The Brain, I was thinking in installing also 2-Plan, it looks very nice, I do not mind to pay for some modules if they are good, developers have to live and they have families to care for.
If you want them to run on your PCLinuxOS system, no, you can't really protect it. If you must stray outside the repositories, then the onus is on you to do your homework and support yourself. The only way I could think of to "protect" an installation from this would be to maintain a "main" install that is free of non-repo stuff, and run a separate install in a virtual machine or on a separate drive/partition (as Crow mentioned already) for all the stuff you need outside the repositories. These seem to me like they would be expensive solutions in terms of disk space, etc., but may prove to be your best bet.
Maybe someone else would have a better idea? (Or, maybe, we could get some of this stuff in the repos so long as it's not encumbered.)