It is/was legit. Many players got hacked or their towns bugged and all of them had the script. However, I think the virus has been fixed now. Not sure. They used to make it a big deal and now I don't see it anywhere, so I think it may have been fixed.
Over the 2+ years I played Ikariam, that has never happened before, at the best of my memory. It was a first for me.
I'm not sure most people use the Greasemonkey CR Converter now though. Most CRs I've seen are the ones from the Web Version. It is free, no download, works perfectly, and really easy to use. Here is the link to it, check it out:
http://tools.betawarriors.com/ikcrc/
However, if you would like to be completely sure that the Greasemonkey is safe, you should PM a Game Operator and ask them.