Does this mean they are now in control of security clearances?
Yep. Hopefully this is a move to pull security clearances from deep staters and prevent them from getting clearances in the future.
"The order also mandates that the Defense Security Service, which began the process of taking over security clearance IT systems from the Defense Information Systems Agency in March, change its name to the Defense Counterintelligence and Security Agency.
According to the order, the change requires that “no later than June 24, the DCSA shall serve as the primary entity for conducting effective, efficient and secure background investigations for the federal government for determining whether covered individuals are or continue to be eligible for access to classified information or eligible to hold a sensitive position."