Hobie actually uses stainless steel rivets for all fittings. However, for this application, replacing with aluminum rivets is acceptable if not preferred, IMO. There is very little load on these rivets since all they do is prevent the end cap from falling out. And you're right, the use of an aluminum rivet will eliminate galvanic corrosion. Also, aluminum rivets are cheaper, easier to pop, and available at your local hardware store. Plus, they will be easier to remove if you have to service the outhaul in the future. I would NOT use an aluminum rivet for any high-load applications, but for the aft boom end cap, aluminum is a fine choice.
If you've never drilled out a rivet before, it can be a challenge. What you want to do is drill off only the head. To do this, I usually use somewhere between a 1/4" to 3/8" drill bit. Also use cutting oil or some form of lubrication when trying to drill through stainless. Once you get the head removed, use a punch to drive the remaining portion of the rivet into the boom and release the end cap.
One more thing, the length of the bungee cord depends on where you locate the outhaul cleat since that is the tie-off point. I would figure out where you want the cleat, then figure out how long the bungee needs to be.