I have marks on my 74 CB550 cases similar to yours. I, too, was told by the parts counterman at Honda to use an o-ring chain on the CB550. Fortunantely, I caught the interference before it was too late. For years, I've been telling people over on the SOHC4 mailing list not to try this on the 550 and have been informed by a couple people they did it and it works fine.
I never believed them, though. As, there are obvious and demonstrable clearance issues. Not everything you read over the internet is true.
I haven't tried this, but I understand that you can use a narrower 520 O-ring chain on the 550. But, you'll have to replace the front and rear sprockets with the compatible narrow toothed alternatives for the whole set up to work properly.
AFAIK the cases have to be split to propertly replace that rubber coated plug the chain chewed up.
Probabaly don't have much to lose by trying to patch it with something. Clean it off really well and do a thin coat of JB weld maybe?
What a shame.