Well, I will try to answer my question myself.
From what I’ve learnt there is no easy and gentle ways to exclude plugins on the fly.
Each plugin,if you lucky, has uninstall.php witch executed upon when you click button “delete”. So if you harshly remove plugin it will leave traces in databases. Even if you just only deactivated plugin, plugins data in database still persists. When you just manually removed a plugin from server, WordPress will just only deactivate it, but not remove any leftover data.
So for now only option is to manually remove plugins, and only after that do execute migration script(in my case it’s managewp). Perhaps in some future hopefully ManageWp will add this functionality.
Which I guess can be achieved..