The Doctor rolled his eyes. He was fairly certain he wasn't going to get through to her. SLA had stolen a great deal from his world, from his peoples creations and discoveries. It wasn't like they were going to perfect stolen Time Lord technology. The Doctor's ego reassured him with that much.
"Did you get what you needed then?" he asked when she seemed to come back, blinking.
He had kept her restricted for a number of reasons, not just because he wanted to keep some information from her but also because the TARDIS was a living being. Plugging into the TARDIS directly could have been overwhelming. The TARDIS might have gotten curious about Annie and looked into her via the connection and that could have been overwhelming. The Doctor did what he did to not only protect himself but her.