You are jumping to conclusions. Pagliano was a political appointee hired at Hillary's request. He was working for both the State Department and privately for Hillary. All of his communications may have been done thru the private email server and a private email account.
There were only two emails found for Pagliano. One was a birthday greeing from Pagliano to Hillary.
Found: At Least One Pagliano Email Sent Directly to Clinton
The State Department announced Monday that the agency found no emails to or from Bryan Pagliano, Hillary Clinton's IT specialist, while Clinton was secretary of state.
However, an email already released by the State Department does show an email from Pagliano to Clinton at Clinton's clintonemail.com address, the email that Pagliano himself set up:
There may not have been any emails to delete from Pagliano's government account. And any deletions from the private server could have been ordered by Clinton. Why did Pagliano take the 5th? This may be the reason.