Best way to protect yourself is to have an image of your OS with all your configurations in place.  If this happens again at that point all that has to be done is re-load the image and you are ready to go.  In order to prevent this from happening again though you would need to determine where exactly the breach was and fix/patch it, and then re-image the newly patched OS.

I had a laptop that I had at work one time, open on my desk, not work related, and I noticed activity on the screen.  The mouse was moving around and someone was able to remote in with TeamViewer and they started to transfer my bitcoin wallet.  They got nothing however as it was passworded and empty at the time.  For a long time I suspected a co-worker because I left my laptop open while I was not around, however I was eventually able to determine that my TeamVIewer credentials were compromised.  I don't install remote access software anymore on any of my coin/mining-related machines.

Use complex passwords and change them frequently, patch known vulnerabilities, don't become lazy or assume your coins are safe today because no one hacked you yesterday.