But does Xander really think it through? Does he genuinely believe that the outcome of 'Faith attacking Angel' is going to be good? Does he see the consequences of what that would do between Buffy, Faith and himself if she actually succeeded in killing Angel?
Or is he just angry and impulsive. Though I still don't think he has that much regard for Faith.
The difference between their manipulation is calculation I think. Xander's thinking strongly resembles the 'kick his ass' comment in that is something done in the moment. It makes it more forgivable.
Here's what I think is happening:
Xander is stewing over guilt. This is why he was out by himself in the first place when he chanced upon Angel. Angel (or Angelus) who murdered Jenny, tortured Giles, and tried to destroy the world (could mention other things, like in season 2 when Angel put him in a headlock when confronting Spike, I can say I wouldn't be quick to forgive and or forget over that, either). Of course he was thrown for a loop.
Then he finds out Buffy has been hiding him (Buffy unfortunately inherited that awful trait from her mother of lying to herself and those around her when it came to the men she was into, and she's lucky the screenwriter gods generally gave her a pass for it, unlike Joyce and all too many women like her in the real world)...and then, if that wasn't enough, she sees Buffy KISSING him. Even without jealousy that should freak him out.
He takes it to the others. He consciously has some valid concerns and angry that Buffy lied to him, while subconsciously sees a way to project his own guilt into Buffy and Angel (so like his own recent romantic deceptions), and thus feel better about himself. This is self-deception and indulgence much as Buffy had been doing earlier. Xander is also the type to be as unforgiving as Buffy in some ways (Buffy was glad that one ghost was caught up in his own hell before she was possessed by him, she should understand better). And seeing them kiss does beg the question of how much further it will go...I'd be upset myself (as were the others) for pragmatic reasons (and as Willow said, Buffy can't see straight when it comes to Angel).
Unfortunately, nothing is resolved. (Perhaps if he overheard what Giles said to Buffy after the rest had left--harsh words which Buffy deserved every one of--he might've been placated enough to not be so angry and bitter while also stewing in his own guilt.) So he was still stewing in his negativity (and subconsciously trying to forget his own guilt so that a lot of his self-hatred transferred to Buffy and Angel) when Faith shows up with her own issues, who has genuinely been manipulated by a diabolical mind that, unlike Xander, cares nothing about justice.
Faith tries taking her hostility out on Xander, only for Xander to give her a new target. Not in the way of Post, but just in bitter anger that speaks his mind. Unlike Post, Xander thinks Angel is a monster (and he has more reasons than Angelus to think so) so when Faith says she's going to kill him, he sees her as on the side of justice, as opposed to achieving some diabolical end or hurting someone he believes is innocent. This is why that when he finds Giles he doesn't believe it was Angel as there were no bite marks, it wasn't his style...but Faith, also feeling betrayed by Buffy (and likely wanting to show herself the better Slayer) stays the course until Post attacks her (and also worth noting she saw her former Watcher killed, so seeing Angel, vamp-faced, over a fallen Post is going to trigger her and make her think she's on the side of the angels in this case).
Strangely, Xander says "your boyfriend isn't as cured as you thought" when Buffy shows up, though he already stated he knew it wasn't Angel who attacked Giles. This speaks to me of his bitterness. But it's not open manipulation the way Post was, it was dysfunctional teenage passions in him and Faith both (as it was Buffy earlier).
In short, Xander is flawed like the rest of the cast (I'll ignore Oz here). Buffy screwed up, and then so did Xander and Faith. Unlike Post there was no grand manipulation or scheming, it was just emotions run amok making them do things they'll regret later. That's part of being human....and making a compelling story.