Personally, pirate and Pather crises being infinite makes sense to me. Not all pirates are under Kanta, although most are scared of her, and I'm sure some idiot thinks they're hot stuff and can raid the player's fortress system.
Pathers likely understand just how dangerous technology can be, so if you are using a lot of it, it sort of makes sense they'll continue to try to destroy it. They are a terrorist organization, so there is pretty much no reason for them not try to take out Moloch, unless something else was given to them. Even then, the Path is pretty loose, so some Pathers will still likely try to wipeout technology, or potentially raid it to steal said tech.
For how the deals would work, I could see them reducing event progress by a large, but not insurmountable, amount. If you have an ungodly amount of AI cores or haven't bothered protecting your system, a deal likely won't completely save you from the Path or pirates.
Normal factions only having one crisis makes more sense, due to diplomacy, PR, etc.