These people are typically the true believers in the Republic. They also believe they are taking down existential threats to the republic. Finally, they believe in defense in layers.
You know what they don't believe in? Playing fair.
No. I wouldn't count on new homeland security leadership appointees having a "free hand" in practice. All of them will discover that their phone, internet and location activity is known to the security agencies. All of that information is also known for their associates. Couple that with the fact that you're dealing with new appointees whose ideology is essentially based more in superiority rather than patriotism, and it points to a lot in that data trove that would be of interest to the kind of people who keep the FBI running from the shadows.
In fact, my bet is that this series of appointees will be far more easily controlled than ones appointed by some red, white and blue boy scout with a martyr complex like McCain would have been for instance. I'd wager there are probably some people in our homeland security infrastructure who actually prefer our appointed leadership be comprised of people who are more malleable.