No, Pro updates are not included in the Framework. You need to update it separately, and it’s not from the Plugins manager, but from the Pro updater that pops up at the top when it notices the Framework’s version is ahead of the Pro one. Or you can get it from your s2member.com Account page and upload it to your site (e.g. via Plugins > Add New). I haven’t built an auto-update feature for the Pro add-on yet.
Some releases ago I changed the thing that deactivated Pro if its version wasn’t matching the Framework, because I didn’t think it made sense: If it was so vital to update, deactivating it didn’t improve the situation, and if it wasn’t vital, deactivating it certainly worsened the situation. So I require a relatively recent Pro version, from last year.
Updating is up to you, but recommended and encouraged to have the latest version.