Ok, so basically it is possible to include extensions with addons in the workshop now. Extensions being a potential risk is nothing new. The fact that addons are automatically updated and the fact that users are not warned about extensions incuded in the addon are new. I do not think that support for extensions should be removed. I think users should have fair warning about their inclusion.
My proposed solution would be that there is a forced warning banner on the steam workshop page with a disclaimer. There also shouldn't be automatic updates for addons with extensions. There should be a prompt when those addons have updates. There should also be warnings when addons that previously didnt have extensions, add extensions.
There is the potential for someone to make a decent addon, then when it gets popular, add a malicious extension with hardly anybody noticing.