Security wise there will be a very visible security note on login page, before any JS code of a plugin was loaded. Same note is also placed very prominently in the plugins folder
. After logging in a user has to know what he/she is doing.
I could imagine that there will be some kind of app/plugin store/repository, where trusted users from the Nxt community curate a selected set of plugins to make sure these can be used safely. For the more prominent ones like MGW the trust level is more or less the same like for the NRS client itself (where you also have to trust some people).
And when account control is released, security situation relaxes a lot, then it will be possible to use plugins just in 2-factor-authentication secured environments and a plugin can't alone control/issue a transaction.