I completely understand that plugins are disabled while printing, but given that the printer can be tied up for hours, it would be really cool if we could queue plugins to be installed after a print completes.
I often read bout octoprint updates and plugins after I've opened it to do a print. I want to do the print, and while it prints I do the reading, want to install, but I can't, so I forget about it.
I think this feature request exists in the project's github issue tracker. You might want to add on to that one.
I know @Charlie_Powell has been doing some updates recently to plugin manager, maybe he knows enough to possibly implement something in software update plugin.