No matter what if your running a program, be it linux or windows (on wine) it always has the potential to mess up things that the user running it has access too.
Not true - you should be running in a SELinux sandbox to solve this problem. I'm not sure if the technology is mature enough for this, but it can and will constrain beyond user privs.
So if you run it as a normal user the worst it can do is mess up that users files All of your important system files are owned by root (or they should be...)
Quite the opposite in fact - anything important's already in the user's files - saved passwords, crypto keys, personal data, financial files. The root stuff is not interesting at all, except as a means to get to the user's files.
- Ivan