Mr. Blunt is, as his name implies, a very blunt man. He's portrayed as emotionless, untrustworthy, and cold—it's kind of weird that he's a good guy, then, right? And the thing is, Mr. Blunt seems like he is a bad guy when we first meet him—his "expressionless" face and "completely empty" eyes makes Alex's "skin crawl" (1.34-35) when they first meet at Ian's funeral. Even after Alex learns that they're on the same team, he can't shake his feeling of unease around Mr. Blunt.
To be honest, Alex might not be wrong to be skeptical. We're shown time and time again how callous Mr. Blunt can be—he even states that Alex dying could be a good thing because "it will be the final proof that there is something wrong" (6.19). Would a nice guy really send a fourteen-year-old (even one as well-trained as Alex) to almost certain death? We're not sure.
Remember: Alex only agrees to become a spy for MI6 after they blackmail him. So, yeah, they might be on the same team, but they're not always working together. In the world of international espionage, even the good guys aren't that good.