Yes it is very easy to go running. In the mornings and evenings there are normally lots of people running around the shores of the lake, or for something a little less flat you can head down the banks of the Rhone.
I would say Geneva is safer than the vast majority of other cities in the world, but of course there are very occasional problems. One specific area I have heard of is during winter evenings in the Jardin Anglais, although I believe this is more related to bag snatching. As a male, I have run through there many times without any problems, and if you are concerned you can just follow the road around the outside instead.
In short, you should not have any concerns about going running around Geneva.