Correct, in this scenario you would be sending the Journey email twice to that Email address.
This actually is one of the core reasons why there exists a unique identifier for contacts, so that you could, if needed, send multiple emails to the same Email address.
Whether a subscriber appears multiple times on a list, group, or data extension to be sent a message. Subscriber key allows an email address to be included multiple times related to different subscriber key values.
In order to send to only one Contact as you've described as the desirable result, you can pick either solution below:
1) Set the Email field as Primary Key in your target Data Extension, this way only unique Email addresses are allowed to be added.
2) You modify the SQL query to update the target Data Extension by using
PARTITION BY command.