I both use ROT13 in my own comments AND find myself agreeing with you. It does make the comments section look a bit of a mess and could be off-putting to first-time visitors to the site.
I suppose we have to ask ourselves why people use it. They want to hide potential spoilers.
Puzzling is unique on SE in that people reading the questions don't usually want an instant answer. They want a try at figuring it out themselves. We use the spoiler tag to hide details in our answers, but this can't be used in comments, and comments on Puzzling serve the same purpose as everywhere else - to improve the answers. They do need to be hidden in some way.
Spoiler tags cannot be used in chat, so moving discussions there doesn't solve the problem, it just moves it. In fact, there would be no warning to either first time visitors nor seasoned puzzlers that clicking into a chat page might contain spoilers. ROT13 or something similar would just have to be used there, and it would look just as messy and be just as off-putting. Okay, so more people visit the main question pages, but everything negative you can say about ROT13 on the site still applies to chat.
Also, from my experience on other SE sites, once someone suggests that a discussion in comments be moved to chat it usually ends there. That can be a good thing - on some sites users get into arguments about different opinions. On Puzzling though that isn't usually the case - people aren't pushing opinions, just swapping ideas to improve answers and solve puzzles with a "hive-mind" mentality. It is a big part of the community to force into hiding on "chat".
I could understand abolishing ROT13 comments if there were some other way of masking spoiler comments that is no less "secure" than the spoiler tag.
On the other hand, would it be right to prevent two people from communicating in comments in any other language we did not understand? That would be linguistic discrimination. If two people want to communicate to each other in ROT13, should we stop them??