I'm just checking out that plugin now (awesome plugin btw) and turning on JS remembers that hostname for the future. I haven't dug into the code yet though so can't vouch for its safety..
Yeah, I whitelist things like github, gmail, etc. But it's a very short list. Everything else loads without JS by default. I can turn it on with a click if I want to so it's a minor inconvenience when I reach a site and I need it. Also, the extension will remember which sites I have turned it on for. I have < 100 sites whitelisted. YMMV.