You are doing the best thing
You could also use JB weld to cover the rivet heads that are loose or missing and that will make a long lasting fix.
But the best thing is what you are doing. As long as you can easily reach the rivets to drill them out and install new one then I think that the best fix in the long run.
I would do that on my boat but I can't reach the rivets without tearing out the floor and the side walls on my boat. And that is a job for the guys at the factory that built the boat not me. That why I either had the missing rivet head holes welded shut by an experienced aluminum welder or put JB weld over the holes and the loose rivet heads.
JB Weld works great as long as you clean the aluminum before you put the JB weld on.