Ignoring a traitor mission will make FIA lose 30% of their resources, it's heavy depending on what you've got in the box. So, penalty decreasing is not heavy if you manage well.

The frequency, it's as random as others. Probably when more assasination missions are in the pool it will be less frequent.

In three days the traitor has time enough to tell CSAT everything about Petros, even the size of his underwear.

This is somewhat problematic though, because if you want to use the campfire and advance 8 hours, you lose all open missions. This limits your options quite a bit.

Furthermore, in Kill the Traitor missions, the traitor should not run away unless he or his guards are alerted. This way, you can go and plant bombs on the building, or fire/throw grenades through a window if you sneak up. I don't know if this is already the way it is, but it seems like they usually drive away when you get close, even if they don't spot you.

I agree that the mission is quite common. I feel like someone flips to the AAF almost as quickly as I accumulate HR points (at least in early game). The mission tends to be quite easy, though, as in towns you can sneak up on the building quickly and easily and if you're lucky and the building is away from civilians you can just mortar the crap out of it from a KM away.

I haven't experienced the problem you're having with the traitor running away too soon, even when i get into firefights with an unrelated patrol of enemies a couple hundred meters away.

I think the fact that it makes you divert from your current operation is just a pain for SP players but it's the reality. You can't be everywhere at once.

The way I think about the traitor missions is that they're debriefing him in a safehouse before moving him to a base or to friendly territory. Some sympathetic citizen in town spotted this and reported it to you. So basically you have about as much time as it takes to debrief the traitor before he's gone forever and the damage is done. All that said, I have a suggestion for you, barbolani:

Would it be possible to make the traitor mission's frequency decrease with each time you complete it? The reason I ask is you keep murdering these guys but they never learn. If you prove to your FIA brothers that you will absolutely kill anyone that betrays them you would think it would make it less likely that people will flip to the other side. Obviously, you can put a floor on the number so that traitor missions still spawn they just become less likely if you consistently do them - maybe they can tick up in chance to spawn each 10 minute check? It's similar to the AAF Attack early on where you have control over the frequency somewhat by where you focus your efforts.

Frequency will be solved on next patch by adding another sidemission on the assassination group. So chances will be less.

They don't learn, well, you are in the mug, no matter how many traitors you kill, AAF executes also everyday FIA supporters, so they can be more afraid to them than to you.