From what I've researched the only real difference is how close you have to be to your object to take the pictures.
It's true that the 100mm lens lets you shoot from twice the distance as the 50mm lens and get a similar composition. That's because the angle of view for a 50mm lens is twice that of a 100mm lens. But the composition won't be exactly the same -- different focal lengths have different effects on an image.
Think about this: imagine that you're taking a regular, non-macro photo of a group of friends who are all standing together. With a wide angle lens, you can stand just a few feet away and get everyone in the shot. With a telephoto lens, on the other hand, you have to stand farther back to fit everyone in the frame. You get a similar composition, since everyone fits in both shots in the same relative arrangement. With the wide angle, though, there's a big difference in the way you see the people in the middle of the frame versus the ones at the edges. You're looking at the person in the center of the frame straight on, but you see the people at the edges at a fairly severe angle -- you probably see only one side of their nose, and you certainly won't see the ear on the side that's farthest from you. With the longer lens, on the other hand, the difference in the angle at which you see everyone is much smaller -- you see everyone more or less straight on. Also, because you're standing relatively far away from everyone, differences in front-to-back distances between the people in the frame seem much smaller than when you're shooting closer.
So, all that's to say that for reasons of simple geometry, the two lenses will give somewhat different looks. It's also worth pointing out that for similar reasons, the longer lens will afford greater depth of field at the same f-stop.
As a novice/intermediate photographer, is it worth spending nearly $500.00 more for that extra 50 mm?
Consider that the difference in price covers a lot more than the difference in focal length. The 100mm you're considering is an L-series lens, i.e. top of the line, built to perform very well under heavy everyday use by professional photographers. And as you point out, it also features image stabilization. In short, this is a lens aimed at pros with a price tag to match.
A better comparison would be to the EF 100mm f/2.8 Macro USM, which is closer to the 50mm Macro in construction and also lacks image stabilization. The difference in price between the 50mm and this 100mm is more like $250. And as others have pointed out the EF-S 60mm is another lens you should consider.