Yes, it should still be usable in manual focus. On Nikon bodies like the D5000, the green focus-confirm indicator can blink when the image is far out of focus or when the selected AF point is on a low-contrast subject, even with manual-focus use. When focus is achieved under the selected point, it should usually light steadily.

A good first step is to set the Sigma lens to MF using its AF/MF switch. If needed, flip the switch a few times in case the switch or contact is not registering properly.

If the lens still behaves oddly, test it on another camera body. Based on the community replies, there may be a compatibility issue with this Sigma 24-70 EX DG on Nikon bodies without an internal focus motor, or the lens itself could have a fault. In short: manual focus should work, but persistent blinking by itself doesn’t necessarily mean the lens is unusable—it may be normal focus confirmation behavior, a switch/contact issue, or a compatibility problem.