For the average user, it is probably isn't a good idea. Then again if you backup your data (like you supposed to), and are safe in your browsing habits then I don't see any real problems with cleaning that out.
Because the problem is that it keeps way too much back history. If your machine is functioning perfectly, a good clean up keeps it running. Even removing System Restore points is a good way to do that.
Most people would never go back three months for a system restore because that would end up breaking things they have legitimately installed (like Windows Updates, etc.)
I wouldn't disable it permanently unless you're willing to deal with the PC when things go faulty without having a restore point to try.
So, in my opinion, disable it then enable it and create a good restore point to clean up the machine is fine for a functional PC.