Exactly you need to provide the credit card info for the agent booking your reservation either with their Sabre etc system or directly with the vendor especially for cruises, airline tickets and tour packages where a deposit and final payment will be made.

Travel Agents for the most part cannot keep credit card numbers unless the client specifically requests auto pay for the final payment and the vendor offers that service.

When I booked cruises with a Travel Agent they asked for the credit card info to hold the cabin and lock in the rate and then called 1 week before final payment to take the credit card number again for final payment.

You can also request the travel agent to call in your deposit and final payment rather than use the electronic system.