Okay! Wifi's back, time to address dem concerns.

[U]Stats[/U]
No arguments. Nerfing B/C+ to C and C-.

[U]Throwing - Daggers[/U]
Wasn't really aware of the stat requirements were higher or lower than the B-Rank 'daggers are comparable to bullets'. So I used Zero Lancer's bullet blocking as my reference point. The END stat clause was there because I felt the need to add a stat to help out the slower Servants.

Would 'daggers are now propelled at speeds two times faster than bullets/at speeds that give even the fastest Servants trouble' work? 

[U]Zabinaya[/U]
B+ Rank was because the [i]other[/i] 'get lots of Assassin mooks' Zabinaya was of equal rank. 

As for Servant-level stats... I'm gonna nerf them to something more like 'base/slightly enhanced human stats' and get rid of the Class/Personal Skills. In hindsight, the anonymity makes for a better PC than the actual PC, and nobody's gonna be carrying around knives to throw... Nobody sane, at least. For the technical knowledge skills, I think some of that can be justified by having Assassin point out that, yes, you stab the armored man's friend, not the armored man himself. But I'll probably get rid of those as well.

Well, since now they don't pose a credible threat to Servants any longer, I'm probably going to have to make more use of the spy network and the morale decrease for having Good-aligned Servants kill a bunch of innocents.

As for the 'Assassin Apocalypse' scenario, I probably should have clarified my meaning of 'take direct control'. If you've played Mass Effect 2, Harbinger is to the Collectors what Assassin is to his Agents. He can only choose one to carry around his indoctrination ability. So rather than the exponential situation, it's more 'Assassin takes control of one guy to infect several others before calling it a day'. Though, the mass sleeper agents concern is still valid, so I figure I can cap it at somewhere around... 100-150 at a time? Somewhere there. That would still give Assassin a decent network, especially if he affects the right people to keep an eye on the other teams. 
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I think that covers all the concerns posed? If I missed anything, you have a suggestion, or I still have a problem, then please point it out.