BuddyPress.org

First, before doing anything, always read the readme.txt file that comes with the install package–this includes the WPMU and the BuddyPress packages. It has important information–especially about what you need to do with the theme files.

Since BuddyPress resides in its own directory, I would suggest deleting the old install. You should not have any issues if you do this. Why? Because any of the plugins, themes, or custom code that you may be using should exist outside of the BuddyPress directory. Before deleting the BP directory, you need to make sure that you deactivate it in WPMU’s backend.

Furthermore, just in case, it is always prudent to have recent backups of your custom themes and your plugins before deleting anything. You want to be absolutely sure that if you accidentally delete the wrong files or directories, that it will not be a big issue since you can simply copy them back. I also suggest that you have a recent copy of your wp-config.php file and even the .htaccess file (assuming that you have plugins installed that may have altered the default congifg).

Since this is a fresh install, I would also suggest starting over with a new DB. If you already have data that you wish to keep in the DB–because you’ve been running WPMU for awhile in a production environment–then your only option is to manually delete the BP tables in the DB before reinstalling BP.

Also, since you are having specific issues with the activity tables, you will need to follow my advice in this post to get the activity tables to reinstall.

As always, before doing anything that affects the DB, please back it up. This also includes backing up your DB before each and every upgrade.

FYI:

https://codex.wordpress.org/Backing_Up_Your_Database

https://codex.wordpress.org/Restoring_Your_Database_From_Backup