A) That's a huge assumption. It's also just a fear of his. There's no proof one way or the other.
B) That's a huge assumption based on a single casual phrase. Does a character's personality change just because they say "Hey," instead of "Hello..."?

You're completely discounting the changes throughout the series. Would the Shinichi we know from episode 1 defend a classmate he doesn't really like who has been a total asshole to him? Would he get the shit kicked out of him to protect Murano from probably getting raped? Would he be confident enough to talk to girls? Would he stab another parasite in the heart to save his own life?

Nah...there's no way he would have done any of that before Migi put 30% of his cells into Shinichi's body.

Give me a break.