Great info from Marret above. As you can see, you aren't the first. I have completely rebuilt badly rusted gutters on my first SMB 'Rusty'. You can see pics of the rebuild deep in the annals of my Rusty build. Probably in my gallery too towards the oldest stuff. By the time you wander through all of the great threads above, though, you'll probably need a nap.
Short answer, fix it now and get it sealed with something. After proper prep I'd personally recommend Rhino/Raptor line up there. I've used Vulkem too to fill gutters.
Welcome to the addiction!