One thought is that such sympathies may go undetected by any initial or active screening processes, whether these beliefs came in their early years or as they served. Mere beliefs, perhaps, without serious action. Otherwise, said agents might just be very good at being sneaky spooks.

Another suggestion is that ONI knows the extent of their sympathies in great detail and will take advantage of it to its fullest effect. That's what I'd do. No point in simply taking them out back and putting one in their head when you can do more with a traitor in your midst.