Javascript is fine, there's liabilities in terms of allowing arbitrary javascript to execute, but Slashdot doesn't and never has allowed that, adding some javascript onto the site is perfectly fine. It's only really a problem when you're allowing XSS and since slashdot doesn't allow javascript in comments you're pretty safe from that unless the site itself gets hacked in which case you're done anyway(you can do anything you could do with javascript on the server side. Heck Slashdot already has plenty of javascript.
The reason the current UI has to go is that it's shit on mobile. They've built a new mobile interface, but it's so vastly different from the dated crap they've got currently coded that they have to maintain two entirely different interfaces which to be honest, costs them more money than the anti-javascript brigade will cost them if/when it leaves. Hell, the current UI is fairly crap on a regular PC.
Even if you believe that Javascript spells a massive change(which it doesn't) a security vulnerability(which it doesn't), or some other horrible violation of your rights, the constant bitching about the new beta is doing more damage the "quality comments' whatever those might be when they're at home than the new UI could even it didn't allow for posting at all, which it does.