Is it too much paranoia to be suspicious of software that require a separate "Helper App"?
All applications sold through Mac App Store have to be sandboxed. Being in a sandbox restricts what the application can do quite a lot. For example they can not access files in folders to which you did not grant them access explicitly via the system Open File dialog. The complete sandbox documentation can be found on the Apple Developer pages, but the important thing to note is that it is very restrictive. 

Having a system tool that can live in it is near impossible. Also note that Apple itself does "cheat" when it comes to the sandbox rule. For example the XCode is accessible via Mac App Store but it is not sandboxed (because it wouldn't work if it were). 

In general though, sandboxing is a good thing. The only way to be really sure if an app is behaving well or not is to see if there were complaints or signs that the developer can not be trusted. Note, however, that before the Mac App Store existed all applications were distributed via other channels and most of the time things went fine.