The LFS person's comment seems a bit harsh without knowing what the rock is. If you can't tell what the rock is, leaving it out is probably safest...but if you can ID the rock type, after soaking it shouldn't be an issue. I've used plenty of non-reef rocks in my tanks without issue; it's turned into some of the best LR I've got.
Something to add onto what Ski said: to be extra safe if you're not 100% sure of the mineral content of the rock (or if you can't see into all the holes in it) check the pH of the water before soaking and periodically over the couple days it soaks. If you see a sharp drop in the pH, that can be an indicator of other trace minerals that you might not want, or decaying organics hidden in places that weren't visible, etc.
EDIT: should also point out that if you want to preserve the fossils in this rock, particularly if it's carbonate-based, an aquarium will destroy it over time. Sometimes the fossils can even be softer than the surrounding rock and dissolve first (not that common, but I've run accross that situation a few times). If the fossils are worth keeping then you might want to save the rock rather than allow reef critters to munch on it.