Overriding the browser default is (almost) never a good idea. As I've mentioned in a previous answer, to hijack this shortcut is recognizing that a user is trying to do a certain familiar function, but aggressively preventing them from doing so, and instead doing something they didn't expect.
One alternative you could try is to unobtrusively inform the user of the additional functionality that your in-app search provides. The user may not be aware that the built-in CTRL+F only scans the loaded data, or understand what that means.
download bmml source – Wireframes created with Balsamiq Mockups
Another option might be to allow the user to opt-in to this shortcut override. In the same unobtrusive style, you might inform the user that your search feature exists, and is available to be bound to the CTRL+F command.