Deleting an activity will remove any associated historical data when creating reports by Enterprise Model (though the data is still available in the data source). Instead of deleting, deactivate the activity by stopping data collection then move the activity to a segregated folder to hide it.

Step by step

Deactivate the collection point

Navigate to Settings > Data sources and click on the name of your data source.
Click Show the setup options dialog in the Setup options tile.

Click Collection points.

Click the pencil (Edit Properties) icon for the activity you wish to deactivate.

Change the drop-down option for Active data collection? to No, skip collecting data for this device id.

Move deactivated activities

Create a child activity/Reporting Rollup Activity folder within the same site of the Enterprise Model that will segregate deactivated activities. 

If named ZZ- it will be at the bottom of the list. 
Click and drag the activity to the folder.
A pop-up will let you know how many people are currently assigned only to the parent activity and will be unassigned, and how many will automatically be added to the new assignment. See Extra Credit.

Clicking the circled number will pop-up a list of the people for review.

Extra Credit

Should I remove people prior to moving/hiding the activity?

While it won't change reporting, best practice is to remove agent assignments from the activity. Otherwise, agents may see an irrelevant activity assignment in their profile.

To remove agents, navigate to Settings > Enterprise Model and select the activity in the tree.

In the People assigned to this activity tile, click Add or remove people assignments.

Click Remove next to each agent. There is no bulk remove (Remove all) option.